---
name: HTSeq
url: http://www-huber.embl.de/HTSeq/doc/overview.html
description: >
  HTSeq is a Python package that provides infrastructure to
  process data from high-throughput sequencing assays.
  HTSeq-count takes a file with aligned sequencing reads, plus
  a list of genomic features and counts how many reads map to each feature.
---

HTSeq is a general purpose Python package that provides infrastructure to
process data from high-throughput sequencing assays. `htseq-count` is a tool
that is part of the main HTSeq package - it takes a file with aligned sequencing
reads, plus a list of genomic features and counts how many reads map to each feature.
