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PASS

Aligns Bi-Seq reads obtained either from SOLiD or Illumina. An accompanying methylation-caller program creates a genomic view of methylated and unmethylated Cs on both DNA strands. The output of PASS-bis is a SAM file that besides the standard mapping information includes an additional field indicating on which of the four possible bisulfite-modified strands the alignment occurred.

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PASS classification

PASS specifications

Software type:
Package/Module
Restrictions to use:
None
Output format:
Modified SAM
Operating system:
Unix/Linux, Mac OS
Computer skills:
Advanced
Stability:
Stable
Interface:
Command line interface
Input format:
FASTQ
Biological technology:
Illumina, Life Technologies, Roche
Programming languages:
C++
Version:
2.30
Maintained:
Yes

PASS distribution

versioning

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No versioning.

PASS support

Maintainer

  • Giorgio Valle <>

Credits

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Publications

Institution(s)

CRIBI Biotechnology Centre; Department of Biology, Università di Padova, Padova, Italy

Funding source(s)

Research supported by the Italian Epigenomics Flagship Project EPIGEN (MIUR/CNR) and by Fondazione Cariparo, Chromus Project

Link to literature

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