FlowgramFixer beta – Model the Ion Torrent Sequencing process

FlowgramFixer beta

:: DESCRIPTION

FlowgramFixer is an improved basecaller for the IonTorrent sequencing platform, which reduces error rates, and generates more uniquely aligned reads and more high quality reads than the default base calling algorithm implemented by IonTorrent in TorrentSuite.

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows / MacOsX
C Compiler

:: DOWNLOAD

FlowgramFixer

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Jul 1;29(13):i344-51. doi: 10.1093/bioinformatics/btt212.
Using state machines to model the Ion Torrent sequencing process and to improve read error rates.
Golan D1, Medvedev P.

IonGAP – Integrated Genome Analysis Platform for Ion Torrent Sequence data

IonGAP

:: DESCRIPTION

IonGAP is a publicly available integrated pipeline designed for the assembly and subsequent analysis of Ion Torrent bacterial sequence data. Both its components and their configuration are based on a research process aimed to discover the optimal combination of tools for obtaining good results from single-end reads generated by the Ion Torrent PGM sequencer.

::DEVELOPER

IonGAP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

IonGAP: integrative bacterial genome analysis for Ion Torrent sequence data.
Baez-Ortega A, Lorenzo-Diaz F, Hernandez M, Gonzalez-Vila CI, Roda-Garcia JL, Colebrook M, Flores C.
Bioinformatics. 2015 May 6. pii: btv283.

PyroHMMsnp 1.1 – SNP Caller for Ion Torrent and 454 Sequencing data

PyroHMMsnp 1.1

:: DESCRIPTION

PyroHMMsnp is a realignment-based SNP calling method for 454 and Ion Torrent sequencing data

::DEVELOPER

Ting Chen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

PyroHMMsnp

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(13):e136. doi: 10.1093/nar/gkt372. Epub 2013 May 21.
PyroHMMsnp: an SNP caller for Ion Torrent and 454 sequencing data.
Zeng F1, Jiang R, Chen T.