FASTQ trimming and error correction

  • FASTX-Tools: Filter and trim fastq files
  • Quake: Error Correction of Short Reads

Aligners and variant callers

  • BWA: Feature rich short read aligner
  • Bowtie: Ultra-fast short read mapping
  • Picard: SAM/BAM alignment filtering
  • SAMtools: SAM/BAM alignment filtering and scoring
  • BCFtools: Utilities for variant calling and manipulating VCFs and BCFs
  • BEDTools: Slice and dice genomics intervals
  • GATK: Variant calling

RNA-seq Analysis

  • kallisto: kmer based RNA-seq quantification
  • TopHat: Spliced alignment for RNA-seq
  • Trinity: De novo transcript assembly and quantification