a pipeline to construct a genome catalogue from metagenomics data
Project description
metapi
A pipeline to construct genome catalogue from metagenomcis data.
Installation
metapi works with Python 3.6+. You can install it via bioconda:
# [WIP]
$ conda install metapi
Or via pip:
$ pip install metapi
Run
help
$ metapi --help
.___ ___. _______ .___________. ___ .______ __
| \/ | | ____|| | / \ | _ \ | |
| \ / | | |__ `---| |----` / ^ \ | |_) | | |
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Omics for All, Open Source for All
A pipeline to construct a genome catalogue from metagenomics data
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
$ metapi init --help
usage: metapi init [-h] [-d WORKDIR] [-s SAMPLES]
[-b {simulate,trimmingrmhost,assembly}]
arguments:
-h, --help show this help message and exit
-d WORKDIR, --workdir WORKDIR
project workdir
-s SAMPLES, --samples SAMPLES
samples list, tsv format required if begin from
trimming, rmhost, or assembly: if it is fastq: the
header is [id, fq1, fq2], else it is sra: the header
is [id, sra] else begin from simulate: the header is
[id, genome, abundance, reads_num, model]
-b {simulate,trimming,rmhost,assembly}, --begin {simulate,trimming,rmhost,assembly}
pipeline starting point
denovo_wf
$ metapi denovo_wf --help
usage: metapi denovo_wf [-h] [-d WORKDIR] [--cores CORES] [--jobs JOBS]
[--list] [--run] [--debug] [--dry_run] [--qsub]
[--wait WAIT] [--snake [SNAKEMAKEARGS]]
[TASK]
positional arguments:
TASK pipeline end point. Allowed values are simulate_all,
prepare_reads_all, raw_fastqc_all, rmhost_bwa_all,
rmhost_bowtie2_all, rmhost_all, assebmly_megahit_all,
assembly_idba_ud_all, assembly_metaspades_all,
assembly_spades_all, assembly_metaquast_all,
assembly_report_all, assembly_all,
alignment_base_depth_all, alignment_all,
binning_metabat2_all, binning_maxbin2_all,
binning_report_all, binning_all, cobinning_all,
predcit_scafitgs_gene_all, predict_bins_gene_all,
predcit_all, checkm_link_bins, checkm_all,
dereplicate_drep_all, dereplicate_all,
classify_short_reads_kraken2_all,
classify_hmq_bins_gtdbtk_all, classify_all,
profiling_metaphlan2_all, profiling_jgi_all,
profiling_humann2_all, profiling_all,
upload_sequencing_all, upload_assembly_all,
upload_all, all
arguments:
-h, --help show this help message and exit
-d WORKDIR, --workdir WORKDIR
project workdir, default: ./
--cores CORES CPU cores
--jobs JOBS qsub job numbers
--list list pipeline rules
--run run pipeline
--debug debug pipeline
--dry_run dry run pipeline
--qsub qsub pipeline
--wait WAIT wait given seconds
--snake [SNAKEMAKEARGS]
other snakemake command options, if want --touch, just
--snake touch
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.
-
begin from trimming, rmhost or assembly:
Paired-end fastq
id fq1 fq2 s1 aa.1.fq aa.2.fq s2 bb.1.fq bb.2.fq s2 cc.1.fq cc.2.fq s3 dd.1.fq dd.2.fq Single-end fastq
id fq1 fq2 s1 aa.1.fq s2 bb.1.fq s2 cc.1.fq s3 dd.1.fq SRA
:
SRA can be dumpped to Paired-end fastq reads
id sra s1 aa.sra s2 bb.sra s2 cc.sra s3 dd.sra -
begin from simulate
id genome abundance reads_num model s1 g1.fa 1.0 1M hiseq s2 g1.fa 0.5 2M hiseq s2 g2.fa 0.5 2M hiseq s3 g1.fa 0.2 3M hiseq s3 g2.fa 0.3 3M hiseq s3 g3.fa 0.5 3M hiseq
It means:
The sample s1 contain 1M reads which come from g1, the relatative abundance of species g1 is 1.0.
The sample s2 contain 2M reads, 1M reads come from g1 and 1M reads come from g2. the relatative abundance of species g1 is 0.5, the relatative abundance of species g2 is 0.5.
The sample s3 contain 3M reads, 0.6M reads come from g1, 0.9M reads come from g2 and 1.5M reads come from g3, the relatative abundance of species g1 is 0.2, the relatative abundance of species g2 is 0.3, the relatative abundance of species g3 is 0.5.
Then metapi will use InSilicoSeq to generate metagenomics shutgun reads.
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. This is the preferred way of getting support. Alternatively, you can mail me.
Contributing
Contributions welcome! Send me a pull request or get in touch.
When contributing a PR, please use the dev branch.
For style, code will be checked using flake8,
black, and
snakefmt. These modules can be
installed via conda, conda install black flake8 flake8-bugbear snakefmt
or via
pip pip install black flake8 flake8-bugbear snakefmt
.
Contributors
- Jie Zhu - @alienzj
License
This module is licensed under the terms of the GPLv3 license.
Project details
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