PiGx: Pipelines in Genomics
What is PiGx?
PiGx is a collection of genomics pipelines. All pipelines are easily configured with a simple sample sheet and a descriptive settings file. The result is a set of comprehensive, interactive HTML reports with interesting findings about your samples.
Wurmus R, Uyar Bora, Osberg B, Franke V, Gosdschan A, Wreczycka K, Ronen J, Akalin A. PiGx: Reproducible genomics analysis pipelines with GNU Guix. Gigascience. 2018 Oct 2. doi: 10.1093/gigascience/giy123. PubMed PMID: 30277498.
PiGx includes the following pipelines:
PiGx BSseq for raw fastq read data of bisulfite experiments
PiGx RNAseq for RNAseq samples
PiGx scRNAseq for single cell dropseq analysis
PiGx ChIPseq for reads from ChIPseq experiments
PiGx CRISPR (work in progress) for the analysis of sequence mutations in CRISPR-CAS9 targeted amplicon sequencing data