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

Assembler Parameters

Parameter	Type	Default	Description
--shovill_assembler	string	skesa	Assembler to be used by Shovill (choices: skesa, megahit, spades, velvet)
--dragonflye_assembler	string	flye	Assembler to be used by Dragonflye (choices: flye, miniasm, raven)
--use_unicycler	boolean		Use unicycler for paired end assembly
--min_contig_len	integer	500	Minimum contig length <0=AUTO>
--min_contig_cov	integer	2	Minimum contig coverage <0=AUTO>
--contig_namefmt	string		Format of contig FASTA IDs in 'printf' style
--shovill_opts	string		Extra assembler options in quotes for Shovill
--shovill_kmers	string		K-mers to use <blank=AUTO>
--dragonflye_opts	string		Extra assembler options in quotes for Dragonflye
--trim	boolean		Enable adaptor trimming
--no_stitch	boolean		Disable read stitching for paired-end reads
--no_corr	boolean		Disable post-assembly correction
--unicycler_mode	string	normal	Bridging mode used by Unicycler (choices: conservative, normal, bold)
--min_component_size	integer	1000	Graph dead ends smaller than this size (bp) will be removed from the final graph
--min_dead_end_size	integer	1000	Graph dead ends smaller than this size (bp) will be removed from the final graph
--nanohq	boolean	false	For Flye, use '--nano-hq' instead of --nano-raw
--medaka_model	string		The model to use for Medaka polishing
--medaka_rounds	integer	0	The number of Medaka polishing rounds to conduct
--racon_rounds	integer	1	The number of Racon polishing rounds to conduct
--no_polish	boolean		Skip the assembly polishing step
--no_miniasm	boolean		Skip miniasm+Racon bridging
--no_rotate	boolean		Do not rotate completed replicons to start at a standard gene
--reassemble	boolean	false	If reads were simulated, they will be used to create a new assembly.
--polypolish_rounds	integer	1	Number of polishing rounds to conduct with Polypolish for short read polishing
--pilon_rounds	integer	0	Number of polishing rounds to conduct with Pilon for short read polishing

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