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https://github.com/mdshw5/fastqp

Simple FASTQ quality assessment using Python
https://github.com/mdshw5/fastqp

bioinformatics fastq kmer-distribution nucleotide-plot python sam

Last synced: 25 days ago
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Simple FASTQ quality assessment using Python

Host: GitHub
URL: https://github.com/mdshw5/fastqp
Owner: mdshw5
License: mit
Created: 2013-09-23T20:01:47.000Z (about 11 years ago)
Default Branch: master
Last Pushed: 2021-05-22T02:00:12.000Z (over 3 years ago)
Last Synced: 2024-11-13T10:38:07.502Z (30 days ago)
Topics: bioinformatics, fastq, kmer-distribution, nucleotide-plot, python, sam
Language: Python
Homepage: https://pypi.python.org/pypi/fastqp
Size: 2.57 MB
Stars: 109
Watchers: 6
Forks: 14
Open Issues: 14
Metadata Files:
- Readme: README.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md

Awesome Lists containing this project

Awesome-Bioinformatics - Fastqp - FASTQ and SAM quality control using Python. (Next Generation Sequencing / Sequence Processing)

README

        fastqp

======

[![Build Status](https://travis-ci.com/mdshw5/fastqp.svg?)](https://travis-ci.com/mdshw5/fastqp)

[![PyPI](https://img.shields.io/pypi/v/fastqp.svg?)](https://pypi.python.org/pypi/fastqp)

Simple FASTQ, SAM and BAM read quality assessment and plotting using Python.

Features

--------

- Requires only Python with Numpy, Scipy, and Matplotlib libraries

- Works with (gzipped) FASTQ, SAM, and BAM formatted reads

- Tabular, tidy, output statistics so you can create your own graphs

- A useful set of default graphics rivaling comparable QC packages

- Counts *all* IUPAC ambiguous nucleotide codes (NMWSKRYVHDB) if present in sequences

- Downsamples input files to around 2,000,000 reads (user adjustable)

- Allows a 5′ and 3′ (left and right) cycle limit for graphics generation

- Tracks kmers and sequence duplication for the *entire* input file

- Plots base call reference mismatches for aligned reads

- Optional sequence duplication calculation using Bloom filters (beta)

Requirements

------------

Tested on Python 2.7, and 3.4

Tested on Mac OS 10.10 and Linux 2.6.18

Installation

------------

    pip install [--user] fastqp

Note: BAM file support requires [samtools](https://github.com/samtools/samtools)

Usage

-----

```

usage: fastqp [-h] [-q] [-s BINSIZE] [-a NAME] [-n NREADS] [-p BASE_PROBS] [-k {2,3,4,5,6,7}] [-o OUTPUT]

              [-ll LEFTLIMIT] [-rl RIGHTLIMIT] [-mq MEDIAN_QUAL] [--aligned-only | --unaligned-only] [-d]

              input

simple NGS read quality assessment using Python

positional arguments:

  input                 input file (one of .sam, .bam, .fq, or .fastq(.gz) or stdin (-))

optional arguments:

  -h, --help            show this help message and exit

  -q, --quiet           do not print any messages (default: False)

  -s BINSIZE, --binsize BINSIZE

                        number of reads to bin for sampling (default: auto)

  -a NAME, --name NAME  sample name identifier for text and graphics output (default: input file name)

  -n NREADS, --nreads NREADS

                        number of reads sample from input (default: 2000000)

  -p BASE_PROBS, --base-probs BASE_PROBS

                        probabilites for observing A,T,C,G,N in reads (default: 0.25,0.25,0.25,0.25,0.1)

  -k {2,3,4,5,6,7}, --kmer {2,3,4,5,6,7}

                        length of kmer for over-repesented kmer counts (default: 5)

  -o OUTPUT, --output OUTPUT

                        base name for output files (default: fastqp_figures)

  -ll LEFTLIMIT, --leftlimit LEFTLIMIT

                        leftmost cycle limit (default: 1)

  -rl RIGHTLIMIT, --rightlimit RIGHTLIMIT

                        rightmost cycle limit (-1 for none) (default: -1)

  -mq MEDIAN_QUAL, --median-qual MEDIAN_QUAL

                        median quality threshold for failing QC (default: 30)

  --aligned-only        only aligned reads (default: False)

  --unaligned-only      only unaligned reads (default: False)

  -d, --count-duplicates

                        calculate sequence duplication rate (default: False)

```

Changes

-------

See [releases page](https://github.com/mdshw5/fastqp/releases) for details.

Examples

--------

![quality heatmap](https://raw.github.com/mdshw5/fastqp/master/examples/example_qualmap.png)

![gc plot](https://raw.github.com/mdshw5/fastqp/master/examples/example_gc.png)

![gc distribution](https://raw.github.com/mdshw5/fastqp/master/examples/example_gcdist.png)

![nucleotide plot](https://raw.github.com/mdshw5/fastqp/master/examples/example_nucs.png)

![nucleotide mismatch plot](https://raw.github.com/mdshw5/fastqp/master/examples/example_mismatch.png)

![kmer distribution](https://raw.github.com/mdshw5/fastqp/master/examples/example_kmers.png)

![depth plot](https://raw.github.com/mdshw5/fastqp/master/examples/example_depth.png)

![quality percentiles](https://raw.github.com/mdshw5/fastqp/master/examples/example_quals.png)

![quality distribution](https://raw.github.com/mdshw5/fastqp/master/examples/example_qualdist.png)

![adapter kmer distribution](https://raw.github.com/mdshw5/fastqp/master/examples/example_adapters.png)

Acknowledgements

----------------

This project is freely licensed by the author, [Matthew Shirley](http://mattshirley.com), and

was completed under the mentorship financial support of Drs. [Sarah Wheelan](http://sjwheelan.som.jhmi.edu)

and [Vasan Yegnasubramanian](http://yegnalab.onc.jhmi.edu) at the Sidney Kimmel Comprehensive

Cancer Center in the Department of Oncology.