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Bwa-meth

Aligns bisulfite-treated sequences and compares it to existing aligners. It allows indels, local alignments, and it never writes a temporary-file of the reads to disk, instead streaming the in silico converted reads directly to the aligner and streaming the alignments directly to a well-formatted alignment file suitable for use in downstream tools. In addition, it works well without quality-trimming, thereby reducing storage requirements 3-fold by not creating quality-trimmed or converted reads.

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Bwa-meth versioning

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Bwa-meth classification

Bwa-meth specifications

Software type:
Application/Script
Restrictions to use:
None
Input format:
FASTQ
Output format:
BAM
Operating system:
Unix/Linux, Mac OS
License:
MIT License
Version:
0.2.0
Requirements:
toolshed
Source code URL:
https://github.com/brentp/bwa-meth
Interface:
Command line interface
Input data:
Fastq files
Output data:
Alignment file
Biological technology:
Illumina
Programming languages:
Python
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes

Bwa-meth support

Documentation

Maintainer

  • Brent Pedersen <>

Credits

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Publications

Institution(s)

Department of Medicine, University of Colorado Denver, School of Medicine, Denver, CO, USA; University of Colorado Cancer Center, Molecular Oncology Program, Aurora, CO, USA

Funding source(s)

This was funded by R01 HL097163, R01 HL101251, 1I01BX001534, RC2 HL101715, N01 AI90052, and S10 RR031832.

Link to literature

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