WG3: Software


Design and implementation of software or software platforms for efficient and versatile analysis of next generation sequencing data. Links to existing tools are posted below. Please try to keep the list organized.

Software Tools

Tool Purpose Author(s) SEQwiki
cutadapt removing known adapters before mapping Marcel Martin (TU Dortmund)
MPscan mapping exactly reads without genome indexing Eric Rivals (CNRS Montpellier)
Gk-arrays indexing collections of reads (library) Eric Rivals (CNRS Montpellier)
Chipster Biologist-friendly NGS data analysis and visualization software Eija Korpelainen et al (CSC) Chipster
RSAT Regulatory Sequence Analysis Tools software suite Jacques van Helden et al (ULB)
peak-motifs A specialized workflow for motif analysis in full-sized sets of ChIP-seq peaks Jacques van Helden et al (ULB) peak-motifs
Utopia Includes a PDF reader that integrates analysis/visualisation tools directly with scientific articles Utopia Team (UniMan)
eSysbio Virtual collaboration workspace for integrated data analysis using standardized tools eSysbio Team (Bergen)
bcbio-nextgen Automated, distributed analysis pipeline for nextgen sequencing Science For Life Laboratory (Stockholm)
J-Express Expression data analysis site The Norwegian Bioinformatics platform (Bergen)
overlapfilter filtering adapters before read alignment Veli Mäkinen (U Helsinki)
readaligner BWT read aligner implementing e.g. suffix filter with Myers' bitparallel k-errors algorithm SuDS group (U Helsinki)
GCSA BWT read aligner with finite automaton representation of reference + SNPs Jouni Sirén (U Helsinki)
Overlap tool all-against-all suffix/prefix alignment for creating overlap graphs for de novo fragment assembly Niko Välimäki et al. (U Helsinki)
Coral Error correction for reads from base space DNA sequencing platforms Leena Salmela et al. (U Helsinki)
Hybrid SCHREK Error correction for reads from base and color space DNA sequencing platforms Leena Salmela (U Helsinki)
MIP Scaffolder Mixed Integer Programming -based contig scaffolder using mate pair data Leena Salmela et al. (U Helsinki)
TAPyR Read mapping Fernandes et al. (INESC-ID/IST Lisbon) TAPyR
Seal Hadoop-based HTSeq data processing (read demultiplexing, mapping, sorting, and base quality recalibration) L. Pireddu et al. (CRS4)
NOIseq Differential expression analysis in RNA-seq robust for sequencing depth bias A. Conesa et al. (CIPF)

Chairs and Members


  • Eija Korpelainen
  • Steve Pettiffer


  • Jose R Valverde
  • Sven Rahmann
  • Andreas Gisel
  • Ralf Herwig
  • Peter Rice
  • Athanasia Pavlopoulou
  • Theodoridis Evangelos
  • Kjell Petersen
  • Petr Baldrian
  • Terri Attwood
  • Guy Perriere
  • Ana Teresa Freitas
  • Ana Conesa
  • Eric Rivals
  • Jacques Van Helden
  • Roman Valls Guimera
  • Robert Lyle
  • Luca Pireddu
  • Aleksi Kallio
  • Bastien Chevreux
  • Simon Heath
  • Claudia Angelini
  • Dimitar Vassilev
  • Ivan Minkov
  • Lucjan Wyrwicj
  • Nuno Roma


(WG members, please create sub-pages of this page for any news item. Put a link here in a list, sorted by date.)

SeqAhead Parallel Computing Task Force documents:

Last modified: 2014/05/08 12:37 by Eija Korpelainen
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