FASTQ QA/QC
BAM QA/QC
ChIP-seq
- MACS2
- diffBind (differential binding)
- CEAS (annotation)
- Ngs.plot (visualization)
RNA-seq
- DESeq2
- EdgeR
- HISAT2
- StringTie
- Sailfish
- featureCount
Variant analysis
NGS utility tools
- BEDtools
- BAMtools
- Picard
- SAMtools
Text and general molecular biology utility tools
- File format converters
- Sequence retrieval
- Operate on Genomic Intervals
- EMBOSS Molecular Biology Tools