Tag: Bisulfite-treated Read

BisPin and BFAST-Gap – Mapping Bisulfite-Treated Reads

BisPin and BFAST-Gap

:: DESCRIPTION

BFAST-Gap is a modification of the BFAST short DNA read trimmer. BFAST-Gap adds functionality for Ion Torrent DNA reads.

BisPin is a Python 2.7 program that uses BFAST-Gap (or BFAST) to map bisulfite-treated short DNA reads to a reference genome. It supports the hairpin construction strategy and rescores ambiguously mapped reads. Its default alignment scoring function is biologically motivated.

::DEVELOPER

Professor Zhang Liqing’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

BisPin

:: MORE INFORMATION

Citation

BisPin and BFAST-Gap: Mapping Bisulfite-Treated Reads
Jacob Porter, Liqing Zhang
bioRxiv 284596; doi: https://doi.org/10.1101/284596

Sherman 0.1.8 – Bisulfite-treated Read FastQ Simulator

Sherman 0.1.8

:: DESCRIPTION

Sherman is a script to simulate high-throughput sequencing data. It specialises in generating libraries for bisulfite-sequencing (BS-Seq) and introducing various sources of contamination which are commonly found in various Next-Gen Sequencing applications.

:: DEVELOPER

Babraham Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX/Windows
  • Perl

:: DOWNLOAD

 Sherman

:: MORE INFORMATION