ismapper
Tags: insertion-sequences transposons comparative-genomics bactopia-tool
Identify insertion sequence positions in bacterial genomes.
This Bactopia Tool uses ISMapper to identify transposase insertion sites in bacterial genomes from short read sequence data.
Usage
Bactopia CLI:
bactopia --wf ismapper \
--bactopia /path/to/your/bactopia/results
Nextflow:
nextflow run bactopia/bactopia/workflows/bactopia-tools/ismapper/main.nf \
--bactopia /path/to/your/bactopia/results
Outputs
Expected Output Files
<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│ └── tools
│ └── ismapper-<TIMESTAMP>
│ └── is1016.fasta
│ ├── logs
│ │ ├── <SAMPLE_NAME>.log
│ │ ├── nf.command.{begin,err,log,out,run,sh,trace}
│ │ └── versions.yml
│ └── supplemental
│ └── IS1016V1_IS1595_IS1016
│ ├── <SAMPLE_NAME>_IS1016V1_IS1595_IS1016_left_final.fastq.gz
│ ├── <SAMPLE_NAME>_IS1016V1_IS1595_IS1016_right_final.fastq.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_10_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_10_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_10_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_11_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_11_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_11_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_12_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_12_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_12_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_13_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_13_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_13_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_14_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_14_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_14_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_15_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_15_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_15_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_16_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_16_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_16_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_17_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_17_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_17_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_18_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_18_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_18_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_19_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_19_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_19_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_1_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_1_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_1_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_20_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_20_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_20_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_21_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_21_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_21_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_22_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_22_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_22_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_23_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_23_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_23_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_24_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_24_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_24_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_25_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_25_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_25_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_26_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_26_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_26_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_27_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_27_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_27_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_28_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_28_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_28_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_29_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_29_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_29_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_2_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_2_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_2_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_30_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_30_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_30_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_31_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_31_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_31_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_32_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_32_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_32_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_33_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_33_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_33_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_34_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_34_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_34_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_35_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_35_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_35_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_36_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_36_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_36_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_37_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_37_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_37_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_38_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_38_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_38_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_39_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_39_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_39_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_3_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_3_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_3_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_40_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_40_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_40_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_41_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_41_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_41_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_42_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_42_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_42_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_43_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_43_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_43_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_44_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_44_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_44_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_45_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_45_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_45_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_46_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_46_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_46_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_47_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_47_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_47_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_48_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_48_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_48_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_49_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_49_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_49_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_4_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_4_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_4_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_50_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_50_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_50_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_51_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_51_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_51_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_52_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_52_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_52_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_53_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_53_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_53_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_54_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_54_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_54_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_55_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_55_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_55_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_56_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_56_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_56_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_57_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_57_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_57_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_58_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_58_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_58_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_59_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_59_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_59_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_5_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_5_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_5_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_60_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_60_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_60_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_61_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_61_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_61_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_62_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_62_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_62_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_63_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_63_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_63_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_64_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_64_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_64_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_65_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_65_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_65_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_66_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_66_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_66_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_67_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_67_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_67_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_68_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_68_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_68_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_69_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_69_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_69_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_6_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_6_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_6_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_70_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_70_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_70_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_71_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_71_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_71_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_72_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_72_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_72_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_73_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_73_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_73_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_74_closest.bed.gz
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│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_74_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_75_closest.bed.gz
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│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_75_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_76_closest.bed.gz
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│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_77_closest.bed.gz
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│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_77_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_78_closest.bed.gz
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│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_78_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_79_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_79_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_79_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_7_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_7_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_7_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_80_closest.bed.gz
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│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_80_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_8_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_8_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_8_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_9_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_9_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_9_table.txt
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_1.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_1.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_10.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_10.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_10_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_10_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_10_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_11.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_11.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_11_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_11_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_11_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_12.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_12.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_12_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_12_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_12_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_13.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_13.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_13_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_13_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_13_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_14.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_14.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_14_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_14_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_14_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_15.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_15.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_15_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_15_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_15_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_16.sorted.bam
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│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_37_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_37_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_38.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_38.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_38_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_38_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_38_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_39.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_39.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_39_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_39_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_39_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_3_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_3_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_3_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_4.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_4.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_40.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_40.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_40_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_40_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_40_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_41.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_41.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_41_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_41_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_41_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_42.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_42.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_42_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_42_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_42_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_43.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_43.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_43_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_43_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_43_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_44.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_44.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_44_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_44_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_44_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_45.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_45.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_45_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_45_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_45_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_46.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_46.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_46_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_46_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_46_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_47.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_47.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_47_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_47_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_47_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_48.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_48.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_48_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_48_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_48_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_49.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_49.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_49_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_49_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_49_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_4_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_4_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_4_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_5.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_5.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_50.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_50.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_50_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_50_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_50_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_51.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_51.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_51_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_51_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_51_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_52.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_52.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_52_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_52_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_52_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_53.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_53.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_53_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_53_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_53_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_54.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_54.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_54_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_54_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_54_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_55.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_55.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_55_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_55_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_55_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_56.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_56.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_56_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_56_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_56_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_57.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_57.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_57_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_57_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_57_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_58.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_58.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_58_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_58_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_58_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_59.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_59.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_59_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_59_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_59_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_5_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_5_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_5_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_6.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_6.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_60.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_60.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_60_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_60_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_60_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_61.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_61.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_61_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_61_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_61_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_62.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_62.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_62_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_62_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_62_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_63.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_63.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_63_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_63_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_63_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_64.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_64.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_64_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_64_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_64_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_65.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_65.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_65_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_65_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_65_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_66.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_66.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_66_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_66_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_66_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_67.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_67.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_67_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_67_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_67_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_68.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_68.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_68_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_68_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_68_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_69.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_69.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_69_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_69_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_69_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_6_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_6_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_6_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_7.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_7.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_70.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_70.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_70_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_70_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_70_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_71.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_71.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_71_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_71_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_71_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_72.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_72.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_72_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_72_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_72_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_73.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_73.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_73_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_73_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_73_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_74.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_74.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_74_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_74_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_74_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_75.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_75.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_75_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_75_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_75_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_76.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_76.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_76_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_76_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_76_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_77.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_77.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_77_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_77_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_77_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_78.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_78.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_78_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_78_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_78_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_79.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_79.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_79_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_79_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_79_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_7_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_7_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_7_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_8.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_8.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_80_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_80_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_80_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_8_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_8_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_8_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_9.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_9.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_9_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_9_merged.sorted.bed.gz
│ └── <SAMPLE_NAME>_right_<SAMPLE_NAME>_9_unpaired.bed.gz
└── bactopia-runs
└── ismapper-<TIMESTAMP>
└── nf-reports
├── ismapper-dag.dot
├── ismapper-report.html
└── ismapper-timeline.html
Per-Sample Results
| File | Description |
|---|---|
*.vcf | VCF file with insertion site calls |
*.txt | Summary of insertion site findings |
Merged Results
| File | Description |
|---|---|
ismapper.tsv | Merged TSV file containing ISMapper results from all samples |
Audit Trail
Below are files that can assist you in understanding which parameters and program versions were used.
Logs
Each process that is executed will have a folder named logs. In this folder are helpful
files for you to review if the need ever arises.
| Extension | Description |
|---|---|
| .begin | An empty file used to designate the process started |
| .err | Contains STDERR outputs from the process |
| .log | Contains both STDERR and STDOUT outputs from the process |
| .out | Contains STDOUT outputs from the process |
| .run | The script Nextflow uses to stage/unstage files and queue processes based on given profile |
| .sh | The script executed by bash for the process |
| .trace | The Nextflow trace report for the process |
| versions.yml | A YAML formatted file with program versions |
Nextflow Reports
These Nextflow reports provide great a great summary of your run. These can be used to optimize resource usage and estimate expected costs if using cloud platforms.
| Filename | Description |
|---|---|
| ismapper-dag.dot | The Nextflow DAG visualization |
| ismapper-report.html | The Nextflow Execution Report |
| ismapper-timeline.html | The Nextflow Timeline Report |
| ismapper-trace.txt | The Nextflow Trace report |
Parameters
Required Parameters
Define where the pipeline should find input data and save output data.
| Parameter | Type | Default | Description |
|---|---|---|---|
--bactopia | string | The path to bactopia results to use as inputs |
ISMapper Parameters
| Parameter | Type | Default | Description |
|---|---|---|---|
--reference | string | Reference genome for typing against in GenBank format | |
--insertions | string | Multifasta file with insertion sequence(s) to be mapped to |
Filtering Parameters
Use these parameters to specify which samples to include or exclude.
| Parameter | Type | Default | Description |
|---|---|---|---|
--include | string | A text file containing sample names (one per line) to include from the analysis | |
--exclude | string | A text file containing sample names (one per line) to exclude from the analysis |
Optional Parameters
These optional parameters can be useful in certain settings.
| Parameter | Type | Default | Description |
|---|---|---|---|
--outdir | string | bactopia | Base directory to write results to |
Nextflow Profile Parameters
Parameters to fine-tune your Nextflow setup.
| Parameter | Type | Default | Description |
|---|---|---|---|
--datasets_cache | string | <HOME>/.bactopia/datasets | Directory where downloaded datasets should be stored. |
Helpful Parameters
Uncommonly used parameters that might be useful.
| Parameter | Type | Default | Description |
|---|---|---|---|
--wf | string | bactopia | Specify which workflow or Bactopia Tool to execute |
--list_wfs | boolean | List the available workflows and Bactopia Tools to use with '--wf' | |
--help_all | boolean | An alias for --help --show_hidden_params | |
--version | boolean | Display version text. |
Composition
This workflow uses the following subworkflows:
- ismapper - Identify transposase insertion sites in bacterial genomes.
Citations
If you use this in your analysis, please cite the following.
-
Bactopia
Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020) -
ISMapper
Hawkey J, Hamidian M, Wick RR, Edwards DJ, Billman-Jacobe H, Hall RM, Holt KE ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data. BMC Genomics 16, 667 (2015)