HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.
HTSeq is described in the following publication (which is currently under review but already available as preprint):
Simon Anders, Paul Theodor Pyl, Wolfgang HuberHTSeq — A Python framework to work with high-throughput sequencing databioRxiv preprint (2014), doi: 10.1101/002824
If you use HTSeq in research, please cite this paper in your publication.
Download links and installation instructions can be found here
The Tour shows you how to get started. It explains how to install HTSeq, and then demonstrates typical analysis steps with explicit examples. Read this first, and then see the Reference for details.
This chapter explains typical usage patterns for HTSeq by explaining in detail three different solutions to the same programming task.
This chapter explorer in detail the use case of counting the overlap of reads with annotation features and explains how to implement custom logic by writing on’s own customized counting scripts
The various classes of HTSeq are described here.
A brief overview over all classes.
In order to represent sequences and reads (i.e., sequences with base-call quality information), the classes Sequence and SequenceWithQualities are used. The classes FastaReader and FastqReader allow to parse FASTA and FASTQ files.
The classes GenomicInterval and GenomicPosition represent intervals and positions in a genome. The class GenomicArray is an all-purpose container with easy access via a genomic interval or position, and GenomicArrayOfSets is a special case useful to deal with genomic features (such as genes, exons, etc.)
To process the output from short read aligners in various formats (e.g., SAM), the classes described here are used, to represent output files and alignments, i.e., reads with their alignment information.
This page describes classes to parse VCF, Wiggle and BED files.
The following scripts can be used without any Python knowledge.
Given a FASTQ or SAM file, this script produces a PDF file with plots depicting the base calls and base-call qualities by position in the read. This is useful to assess the technical quality of a sequencing run.
Given a SAM file with alignments and a GFF file with genomic features, this script counts how many reads map to each feature.
HTSeq is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
The full text of the GNU General Public License, version 3, can be found here: http://www.gnu.org/licenses/gpl-3.0-standalone.html