Starred repositories
Streamlit — A faster way to build and share data apps.
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
Demultiplex Illumina sequencer output via DRAGEN, create fastq files and launch pipelines
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
✅ The 5th major version of the programmer-friendly testing framework for Java and the JVM
A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
A DSL for data-driven computational pipelines
A tool to map bisulfite converted sequence reads and determine cytosine methylation states
A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
NGS Statistics Database with historical Picard Stats, IGO fastq.gz paths and Sequencer Start & Stop Times
Create "haplotype maps" of variants in order to use with Picardtools Crosscheck_Files utility, which allows for robust genotyping of functional genomic data.
Open workflow definitions for genomic analysis from MGI at WUSM.
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.