https://github.com/opengene/dedup

Deduplication for cfDNA sequencing data
https://github.com/opengene/dedup

bioinformatics ctdna deduplication liquid ngs

Last synced: 3 months ago
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Deduplication for cfDNA sequencing data

• Host: GitHub
• URL: https://github.com/opengene/dedup
• Owner: OpenGene
• License: mit
• Created: 2017-07-05T06:56:30.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2017-07-05T07:13:03.000Z (over 8 years ago)
• Last Synced: 2025-04-10T09:54:08.121Z (6 months ago)
• Topics: bioinformatics, ctdna, deduplication, liquid, ngs
• Language: Python
• Size: 3.91 KB
• Stars: 11
• Watchers: 10
• Forks: 4
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# dedup

A small script for NGS data deduplication, optimized for cfDNA sequencing data

# Dependency

This script depends on `pysam` module, please install it by `pip` or `easy_install` first

# Usage

```shell

./dedup.py -1 in.sorted.bam -o out.bam > dedup.log

```

Be sure that the in.sorted.bam is sorted