bactopia_assembler

Tags: bacteria assembly hybrid shovill dragonflye unicycler illumina nanopore sample-scope

Assemble bacterial genomes using short read, long read, or hybrid strategies.

Automatically selects the appropriate assembler based on input read types:

• Short Paired-End Reads: Uses Shovill (SKESA/SPAdes wrapper).
• Short Single-End Reads: Uses Shovill (SKESA/SPAdes wrapper).
• Long Reads: Uses Dragonflye (Flye/Miniasm wrapper).
• Hybrid: Uses Unicycler or Dragonflye (with polishing).

Summary statistics for each assembly are generated using assembly-scan.

Uses named record input with explicit read slots (r1, r2, se, lr, assembly) as Path?.

When runtype is 'assembly' or 'assembly_accession' and --reassemble is not set,

the original assembly is used without re-assembly.

Inputs

record (
    meta: Record,
    r1: Path?,
    r2: Path?,
    se: Path?,
    lr: Path?,
    fna: Path?
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
r1	Path?	Illumina R1 reads (paired-end)
r2	Path?	Illumina R2 reads (paired-end)
se	Path?	Single-end Illumina reads
lr	Path?	Long reads (ONT/PacBio) for long-read or hybrid assembly
fna	Path?	Assembly file (FASTA) for assembly-based runtypes

Outputs

record (
    meta: Record,
    fna: Path?,
    r1: Path?,
    r2: Path?,
    se: Path?,
    lr: Path?,
    tsv: Path?,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
fna	Path?	Assembled contigs in FASTA format
r1	Path?	Passthrough Illumina R1 reads
r2	Path?	Passthrough Illumina R2 reads
se	Path?	Passthrough single-end reads
lr	Path?	Passthrough long reads
tsv	Path?	Tab-delimited report of assembly statistics (N50, length, coverage)
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

Used By

Subworkflows

• bactopia_assembler - Assemble bacterial genomes using automated assembler selection.

Workflows

• bactopia - Comprehensive bacterial analysis pipeline for complete genomic characterization.
• staphopia - Comprehensive analysis pipeline for Staphylococcus aureus isolates.

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)

• any2fasta
  Seemann T any2fasta: Convert various sequence formats to FASTA (GitHub)

• assembly-scan
  Petit III RA assembly-scan: generate basic stats for an assembly (GitHub)

• BWA
  Li H Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv [q-bio.GN] (2013)

• Dragonflye
  Petit III RA Dragonflye: Assemble bacterial isolate genomes from Nanopore reads. (GitHub)

• FLASH
  Magoč T, Salzberg SL FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27.21 2957-2963 (2011)

• Flye
  Kolmogorov M, Yuan J, Lin Y, Pevzner P Assembly of Long Error-Prone Reads Using Repeat Graphs Nature Biotechnology (2019)

• Medaka
  ONT Research Medaka: Sequence correction provided by ONT Research (GitHub)

• MEGAHIT
  Li D, Liu C-M, Luo R, Sadakane K, Lam T-W MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31.10 1674-1676 (2015)

• Miniasm
  Li H Miniasm: Ultrafast de novo assembly for long noisy reads (GitHub)

• Minimap2
  Li H Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34:3094-3100 (2018)

• Nanoq
  Steinig E Nanoq: Minimal but speedy quality control for nanopore reads in Rust (GitHub)

• Pigz
  Adler M. pigz: A parallel implementation of gzip for modern multi-processor, multi-core machines. Jet Propulsion Laboratory (2015)

• Pilon
  Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PloS one 9.11 e112963 (2014)

• Racon
  Vaser R, Sović I, Nagarajan N, Šikić M Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res 27, 737-746 (2017)

• Rasusa
  Hall MB Rasusa: Randomly subsample sequencing reads to a specified coverage. (2019).

• Raven
  Vaser R, Šikić M Time- and memory-efficient genome assembly with Raven. Nat Comput Sci 1, 332-336 (2021)

• samclip
  Seemann T Samclip: Filter SAM file for soft and hard clipped alignments (GitHub)

• Samtools
  Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009)

• Shovill
  Seemann T Shovill: De novo assembly pipeline for Illumina paired reads (GitHub)

• Shovill-SE
  Petit III RA Shovill-SE: A fork of Shovill that includes support for single end reads. (GitHub)

• SKESA
  Souvorov A, Agarwala R, Lipman DJ SKESA: strategic k-mer extension for scrupulous assemblies. Genome Biology 19:153 (2018)

• SPAdes
  Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of computational biology 19.5 455-477 (2012)

• Unicycler
  Wick RR, Judd LM, Gorrie CL, Holt KE Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol. 13, e1005595 (2017)

• Velvet
  Zerbino DR, Birney E Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome research 18.5 821-829 (2008)

Source

View source on GitHub

Version

BACTOPIA_ASSEMBLER:
    - bactopia-assembler: 1.0.5