ChIP sequencing data analysis bioinformatics software tools

Chromatin immunoprecipitation followed by sequencing (ChIP-seq), first described in 2007 (Barski et al., 2007; Johnson et al., 2007; Mikkelsen et al., 2007; Robertson et al., 2007), allows in vivo determination of where a protein binds the genome, which can be transcription…

ChIP-seq analysis steps

Preprocessing & quality control

Data analysis

Visualization & interpretation

File, data & workflows

ChIP-seq analysis workflow

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ChIP-seq analysis workflow schema

Most recent bioinformatics tools

G T A T C G C T A
SeqDepot
Dataset

SeqDepot

Enables users to retrieve and process with minimal effort both primary and…

Enables users to retrieve and process with minimal effort both primary and intrinsic feature data for existing sequences. SeqDepot is a database that assimilates known primary sequences with…

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SMS
Web

SMS The Sequence Manipulation Suite

Allows analysis and manipulation of sequence data. SMS can display the genetic…

Allows analysis and manipulation of sequence data. SMS can display the genetic code, restriction enzyme set and codon usage table it uses that allowing users to make changes before performing an…

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EMBOSS
Desktop

EMBOSS European Molecular Biology Open Software Suite

Gives access to many free software tools for sequence analysis. EMBOSS aims to…

Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit.…

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GSA
Dataset

GSA Genome Sequence Archive

Provides a data repository for archiving raw sequence data. GSA is built based…

Provides a data repository for archiving raw sequence data. GSA is built based on INSDC data standards, structures and provides data archival services for scientific communities. This resource…

Most popular analytical software

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SAMtools
Desktop

SAMtools

A suite of programs for interacting with high-throughput sequencing data. It…

A suite of programs for interacting with high-throughput sequencing data. It can manipulate alignments in the SAM/BAM/CRAM formats : reading, writing, editing, indexing, viewing and converting…

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HOMER
Desktop

HOMER Hypergeometric Optimization of Motif EnRichment

A suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER…

A suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of…

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NGS-QC…
Desktop

NGS-QC Generator

A computational-based approach that infers quality indicators from the…

A computational-based approach that infers quality indicators from the distribution of sequenced reads associated to a particular NGS profile.

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Trimmomatic
Desktop

Trimmomatic

Performs a variety of trimming tasks for Illumina paired-end and single ended…

Performs a variety of trimming tasks for Illumina paired-end and single ended data. Trimmomatic is a flexible, pair-aware preprocessing tool, optimized for Illumina next-generation sequencing (NGS)…

Curators for ChIP-seq analysis

  • Julie Dubois-Chevalier's avatar image
    Julie Dubois-Chevalier
    INSERM UMR1011, University of…
  • Fabien Pichon's avatar image Fabien Pichon's country flag
  • Hélène Dauchel's avatar image
    Hélène Dauchel
    LITIS EA 4108 Computer science,…

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