Bio2m Tools
- Annot2Seq : Web interface to convert a vcf or a bed file to sequences and kmers
- If you have a vcf or bed file convert it to sequences. For vcf file, you will also get the sequences with the variations.
- KmerExploR/KmerTool to generate nice graph from kmer count (using countTags)
- KITE: Using machine learning to filter kmers in RNASeq data and
discover new biomarquers
- 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
Expertise software
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
