nbay13 / toilkit

A python package for working with inputs to and outputs from the toil-rnaseq pipeline

toilkit

A set of Python commands for preparing inputs to and processing outputs from the Toil RNA-Seq pipeline

Uses Python's subprocess module and command line utilities to execute subcommands efficiently

Includes additional commands for dual alignment to human and mouse genome and subsequent mouse read filtering. Pipeline configurations including reference files and directory stuctures designed for shared workstations in the Graeber lab @ UCLA.

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Installation

You can install toilkit using pip:

pip install -e git+https://github.com/nbay13/toilkit.git#egg=toilkit

Commands

toilkit provides a set of subcommands that can be used from the command line. Here's an overview of the available subcommands:

Handling fastqs:

• fastq-merge: Merge fastq files based on sample name
• fastq-rename: Rename fastqs based on key

(optional) mouse read filtering:

• bbseal: Run bbduk (adapter trimming) and bbseal (dual reference alignment)
• bbcat: Concatenate human and ambiguously-aligned reads into fastqs
• bbmetrics: Gather bbseal alignment metrics

Prep toil-rnaseq manifest:

• make-manifest: Create a toil-rnaseq manifest file
• cut-manifest: Split a manifest file into smaller parts
• manifest-key: Convert a manifest file to a sample key .tsv file

Handling toil-rnaseq outputs:

• toil-fix: (if bamQC enabled) Rename outputs with '_FAIL' filename suffix
• toil-combine: Extract info from UUID_XX.tar.gz results -- such as RSEM, QC and/or STAR junctions data
• toil-rename: Final rename of all toil-rnaseq output files

Usage

To use a specific subcommand, run toilkit <subcommand>. For example:

toilkit fastq-merge --indir <input_directory> --outdir <output_directory>

For detailed usage instructions check the tutorial