The fastest VCF/BCF parser in R https://doi.org/10.1093/bioinformatics/btae049

GENE-SWitCH project RNA-Seq analysis pipeline

developpment of pipeline for small RNA

MineYourSymbiont : Targetted genome assembly for metagenomics pipeline.

QuasiModo: Assessing viral genomic analysis methods on HCMV strain mixture

MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.