Bio2m Tools


Logiciels

Développement interne

Kmer tools

  • Kmerator to generate specific kmer to one or more transcript
  • and its viewer compagnion KmerTool
  • DE-kupl to find kmer differentially expressed between 2 samples conditions
  • countTags to count list of kmers

Mapper

  • CRAC, THE Mapper that map and analyse your reads in once pass
  • CracTools, its compagnion brother to extract most of the CRAC data in the bam file

Logiciels utilisés

RNA-Seq

  • STAR, last best RNA-Seq mapper
  • Kallisto, count your genes without mapping
  • Sleuth, differential gene expression analysis made easy

DNA-Seq

  • Hisat2, the last DNA mapper
  • Freebayes, the faster variant caller
  • VEP, an easy way to filter your variant

Kmer

  • Jellyfish, count all your Kmer in a fastq file

Workflow

  • Snakemake, to reproduce your pipeline easily