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FILES MANIPULATION
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Convert Formats
Convert solid to fastq Convert solid to fastq
Wig-to-bigWig converter
BED-to-bigBed converter
NGS TOOLBOX
NGS: QC
Fastqc: Fastqc QC using FastQC from Babraham
NGS: Motif Discovery
(di)ChIPmunk - de novo motif finding
(di)ChipMunk - peak multi-fasta generator
AhoPro Motif search and P-value calculation
NGS: Mapping
NGS: SAM Tools
SAM-to-BAM converts SAM format to BAM format
flagstat provides simple stats on BAM files
Filter BAM on alignment quality values
NGS: BED Tools
NGS: Peak Calling
HMCan Histone Modification detection in Cancer samples
MICSA Motif Identification for Chip-Seq Analysis.
MACS Model-based Analysis of ChIP-Seq
PeakSplitter Subdivides peak regions containing more than one site of signal enrichment
CCAT Control-based ChIP-seq Analysis Tool
FindPeaks a Peak Finder/Analysis application for the ChIP-Seq
NGS: Peak Annotation
NGS: RSAT tools
RSAT Peak Motifs Create Logo images from peaks
RSAT Convert Matrix Inter-conversions between various formats of PSSM
RSAT Matrix Scan Scan a DNA sequence with a profile matrix
RSAT Compare Matrices Comparison between two collections of position-specific scoring matrices
RSAT Oligo Analysis Analysis of oligomer occurrences in nucleotidic of peptidic sequences
RSAT Dyad Analysis Analysis of oligomer occurrences in nucleotidic of peptidic sequences
NGS: SVDetect
BAM preprocessing to get abnormal pairs
Compare structural variants between two samples
Circos plots
Detect clusters of anomalously mapped pairs and identify structural variants