Internal BFSSI package for assembling prokaryotic genomes from short reads
Project description
ProkaryoteAssembly
Two simple scripts to assemble prokaryotic genomes using paired-end reads.
Pipeline Overview
- QC on reads with bbduk.sh (adapter trimming/quality filtering)
- Error-correction of reads with tadpole.sh
- Assembly of reads with skesa
- Alignment of error-corrected reads against draft assembly with bbmap.sh
- Polishing of assembly with pilon
Usage
The first script, prokaryote_assemble.py
, operates on a single sample at a time.
Usage: prokaryote_assemble.py [OPTIONS]
Options:
-1, --fwd_reads PATH Path to forward reads (R1). [required]
-2, --rev_reads PATH Path to reverse reads (R2). [required]
-o, --out_dir PATH Root directory to store all output files. [required]
--version Specify this flag to print the version and exit.
--help Show this message and exit.
The second script, prokaryote_assemble_dir.py
, will detect all *.fastq.gz files in
a directory and run the assembly pipeline on each sample it can pair.
Usage: prokaryote_assemble_dir.py [OPTIONS]
Options:
-i, --input_dir PATH Directory containing all *.fastq.gz files to assemble.
[required]
-o, --out_dir PATH Root directory to store all output files. [required]
-f, --fwd_id TEXT Pattern to detect forward reads. Defaults to "_R1".
-r, --rev_id TEXT Pattern to detect reverse reads. Defaults to "_R2".
--help Show this message and exit.
Python (3.6) Dependencies
- click
External Dependencies
NOTE: All external dependencies must be available via PATH.
Versions confirmed to work are in brackets.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.