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:
Standalone
Restrictions to use:
None
Input format:
FASTQ
Output format:
BAM
Operating system:
Unix/Linux, Mac OS
License:
MIT License
Version:
0.2.0
Requirements:
python (including python3); toolshed library (can be installed with easy_install toolshed or pip install 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:
Basic
Stability:
Stable

Bwa-meth support

Maintainer

Additional information

(Pedersen et al., 2005) Fast and accurate alignment of long bisulfite-seq reads. Bioinformatics. https://arxiv.org/abs/1401.1129

Credits

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.

Investigator(s)

David A. Schwartz

Developer(s)

Brent S. Pedersen, Kenneth Eyring, Subhajyoti De, Ivana V. Yang, David A. Schwartz

Curator(s)

Shaojun Xie

Contributor(s)

Brent S. Pedersen

Link to literature

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