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Aggregate results from bioinformatics analyses across many samples into a single report.
A quality control analysis tool for high throughput sequencing data
PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
A tool set for short variant discovery in genetic sequence data.
bedtools - the swiss army knife for genome arithmetic
C library for high-throughput sequencing data formats
A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Development is …
Tools (written in C using htslib) for manipulating next-generation sequencing data
This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
Official code repository for GATK versions 4 and up