Cimorgh Medical IT Solutions's repositories
civicpy
A python interface for the CIViC db application
cromshell
CLI for interacting with Cromwell servers
fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
gatk
Official code repository for GATK versions 4 and up
Genomics_workflow
MobidicWDL workflows
MDUtils
Utilities for MobiDetails
MobiDetails
WebApp for DNA variants interpretation
Nirvana_source18
The nimble & robust variant annotator
Pangolin
Pangolin is a deep-learning method for predicting splice site strengths.
parabricks-wdl
Accelerated genomics workflows in the Workflow Description Language
pumbaa
Command-line interface for Cromwell server
rest_variantValidator
REST Interface for VariantValidator. Includes docker container
RNA-seq
A BioWDL pipeline for processing RNA-seq data, starting with FASTQ files to produce expression measures and VCFs. Category:Multi-Sample
sambamba
Tools for working with SAM/BAM data
Spring
FASTQ compression
VCFshiny
shiny app to visualize vcf and annovar file
wdl-packager
Package a WDL and its imports into a zip file