An intuitive and efficient tool for preprocessing Illumina FASTQ reads
miRPlant: An Integrated Tool for Identification of Plant miRNA
MiRDeep*
Supervised Ranking of Contigs in de novo Assemblies
A set of tools for working with high-throughput sequencing data
DeNovoCheck: Inheritance analysis for NGS trio data
cnvHiTSeq is a set of tools for detecting CNVs using sequencing data.