BacAssembly

A hybrid assembly pipeline for bacteria

Installation

bacassembly works with Python 3.6+.

[WIP]
$ conda install -c bioconda bacassembly

Or via pip:

[WIP]
$ pip install bacassembly

Run

help

$ bacassembly --help

  ______             ___                         _     _
  | ___ \           / _ \                       | |   | |
  | |_/ / __ _  ___/ /_\ \___ ___  ___ _ __ ___ | |__ | |_   _
  | ___ \/ _` |/ __|  _  / __/ __|/ _ \ '_ ` _ \| '_ \| | | | |
  | |_/ / (_| | (__| | | \__ \__ \  __/ | | | | | |_) | | |_| |
  \____/ \__,_|\___\_| |_/___/___/\___|_| |_| |_|_.__/|_|\__, |
                                                        __/ |
                                                       |___/

             Omics for All, Open Source for All

     Hybrid assembly and polish using short and long reads

  optional arguments:
  -h, --help     show this help message and exit
  -v, --version  print software version and exit

  available subcommands:

  init         init project
  denovo_wf    denovo_wf pipeline

init

$ bacassembly init --help
  usage: bacassembly init [-h] [-d WORKDIR] [-s SAMPLES]
                          [-b {trimming,rmhost,assembly}]

  optional arguments:
  -h, --help            show this help message and exit
  -d WORKDIR, --workdir WORKDIR
                        project workdir, default: ./
  -s SAMPLES, --samples SAMPLES
                        desired input: samples list, tsv format required.
                        header: ["id", "long_reads", "short_reads_1", "short_reads_2"]
  -b {trimming,rmhost,assembly}, --begin {trimming,rmhost,assembly}
                        pipeline starting point

denovo_wf

$ bacassembly denovo_wf --help
  usage: bacassembly denovo_wf [-h] [-d WORKDIR] [--config CONFIG]
                               [--cores CORES] [--jobs JOBS] [--list] [--run]
                               [--debug] [--dry_run] [--qsub] [--wait WAIT]
                               [--snake [SNAKEMAKEARGS]]
                               [TASK]

  positional arguments:
  TASK                  pipeline end point. Allowed values are trimming_all,
                        all

  optional arguments:
  -h, --help            show this help message and exit
  -d WORKDIR, --workdir WORKDIR
                        project workdir, default: ./
  --config CONFIG       config.yaml, default: ./config.yaml
  --cores CORES         CPU cores, default: 8
  --jobs JOBS           qsub job numbers, default: 80
  --list                list pipeline rules
  --run                 run pipeline
  --debug               debug pipeline
  --dry_run             dry run pipeline
  --qsub                qsub pipeline
  --wait WAIT           wait given seconds, default: 60
  --snake [SNAKEMAKEARGS]
                        other snakemake command options(sankemake -h), if want
                        --touch, just --snake touch

Example

# init project
$ bacassembly init -d . -s samples.tsv -b trimming

# run trimming
$ metapi denovo_wf trimming_all --run

# run all
$ metapi denovo_wf --run

input requirements

The input samples file: samples.tsv format:

Note: If id col contain same id, then the reads of each sample will be merged. Note: The fastq need gzip compress.

id	long_reads	short_reads_1	short_reads_2
s1	aa.long.fq.gz	aa.1.fq.gz	aa.2.fq.gz
s2	bb.long.fq.gz	bb.1.fq.gz	bb.2.fq.gz
s2	cc.long.fq.gz	cc.1.fq.gz	cc.2.fq.gz
s3	dd.long.fq.gz	dd.1.fq.gz	dd.2.fq.gz

Getting help

If you want to report a bug or issue, or have problems with installing or running the software, please create a new issue.

License

This module is licensed under the terms of the GPLv3 license.