Bactopia-Sapelo2
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Category
Bioinformatics
Program On
Sapelo2
Version
3.2.0
Author / Distributor
Please see https://bactopia.github.io/v3.1.0/
Description
Bactopia is a flexible pipeline for complete analysis of bacterial genomes. This module can be loaded directly: module load Bactopia/3.2.0-conda
Running Program
Documentation
[cft07037@b1-24 ~]$ ml Bactopia/3.2.0-conda
[cft07037@b1-24 ~]$ bactopia --help
Nextflow 25.10.4 is available - Please consider updating your version to it
N E X T F L O W ~ version 23.10.1
Launching `/apps/eb/Bactopia/3.2.0-conda/share/bactopia-3.2.0/main.nf` [friendly_golick] DSL2 - revision: 0cd9f79ba7
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bactopia v3.2.0
Bactopia is a flexible pipeline for complete analysis of bacterial genomes
---------------------------------------------
Typical pipeline command:
bactopia --fastqs samples.txt --datasets datasets/ --species 'Staphylococcus aureus' -profile singularity
Required Parameters
Processing Multiple Samples
--samples [string] A FOFN (via bactopia prepare) with sample names and paths to FASTQ/FASTAs to process
Processing A Single Sample
--r1 [string] First set of compressed (gzip) Illumina paired-end FASTQ reads (requires --r2 and --sample)
--r2 [string] Second set of compressed (gzip) Illumina paired-end FASTQ reads (requires --r1 and --sample)
--se [string] Compressed (gzip) Illumina single-end FASTQ reads (requires --sample)
--ont [string] Compressed (gzip) Oxford Nanopore FASTQ reads (requires --sample)
--hybrid [boolean] Create hybrid assembly using Unicycler. (requires --r1, --r2, --ont and --sample)
--short_polish [boolean] Create hybrid assembly from long-read assembly and short read polishing. (requires --r1, --r2, --ont and
--sample)
--sample [string] Sample name to use for the input sequences
Downloading from SRA/ENA or NCBI Assembly
Note: Error free Illumina reads are simulated for assemblies
--accessions [string] A file containing ENA/SRA Experiment accessions or NCBI Assembly accessions to processed
--accession [string] Sample name to use for the input sequences
Processing an Assembly
Note: Error free Illumina reads are simulated for assemblies
--assembly [string] A assembled genome in compressed FASTA format. (requires --sample)
--check_samples [boolean] Validate the input FOFN provided by --samples
Dataset Parameters
--species [string] Name of species for species-specific dataset to use
--ask_merlin [boolean] Ask Merlin to execute species specific Bactopia tools based on Mash distances
--coverage [integer] Reduce samples to a given coverage, requires a genome size [default: 100]
--genome_size [string] Expected genome size (bp) for all samples, required for read error correction and read subsampling [default:
0]
--use_bakta [boolean] Use Bakta for annotation, instead of Prokka
QC Parameters
--use_bbmap [boolean] Illumina reads will be QC'd using BBMap
--use_porechop [boolean] Use Porechop to remove adapters from ONT reads
Assembler Parameters
--nanohq [boolean] For Flye, use '--nano-hq' instead of --nano-raw
AMRFinder+ Parameters
--organism [string] Taxonomy group to run additional screens against
--amrfinder_noplus [boolean] Disable running AMRFinder+ with the --plus option
--amrfinder_opts [string] Extra AMRFinder+ options in quotes.
--amrfinder_db [string] A custom AMRFinder+ database to use, either a tarball or a folder
MLST Parameters
--scheme [string] Don't autodetect, force this scheme on all inputs
--minid [integer] Minimum DNA percent identity of full allelle to consider 'similar' [default: 95]
--mincov [integer] Minimum DNA percent coverage to report partial allele at all [default: 10]
--minscore [integer] Minimum score out of 100 to match a scheme [default: 50]
--nopath [boolean] Strip filename paths from FILE column
--mlst_db [string] A custom MLST database to use, either a tarball or a directory
Prokka Parameters
--proteins [string] FASTA file of trusted proteins to first annotate from
--prodigal_tf [string] Training file to use for Prodigal
--prokka_coverage [integer] Minimum coverage on query protein [default: 80]
Optional Parameters
--outdir [string] Base directory to write results to [default: bactopia]
Nextflow Profile Parameters
--datasets_cache [string] Directory where downloaded datasets should be stored. [default: <BACTOPIA_DIR>/data/datasets]
Helpful Parameters
--wf [string] Specify which workflow or Bactopia Tool to execute [default: bactopia]
--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.
!! Hiding 110 params, use --show_hidden_params (or --help_all) to show them !!
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If you use bactopia for your analysis please cite:
* Bactopia
https://doi.org/10.1128/mSystems.00190-20
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://bactopia.github.io/acknowledgements/
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System
64-bit Linux