Example uses of hts nim

additions to this page are very much welcomed!

Example Programs with hts-nim

• (VCF) looking at allele balance on mitochondrial chromosomes: https://gist.github.com/brentp/ac0169cce003ddc8d7b4b50940dc3f42
• (BAM) counting sequence motifs in a BAM: https://brentp.github.io/post/nim-mundane2/
• (BAM+cigar operations) don't pileup : https://brentp.github.io/post/no-pile/
• (Fai for fasta): https://github.com/brentp/hts-nim/wiki/Fai-example

Repos using hts-nim

• [andreas-wilm/quad] mapping base-qualities in bam files
• Avsecz/nimnexus command-line tools for ChIP-nexus data
• SeqOne/kraf kmer-based allele frequency calibration
• SeqOne/clinvcf make a VCF directly from clinvar XML
• papaemmelab/split_bed_by_reads BAM and bed file reading
• danielecook/seq-collection extensive utilities for BAM and VCF
• brentp/duphold annotate an SV VCF with coverage from BAM
• brentp/somalier fast kinship estimation and validation from CRAM/BAM/VCF/GVCF
• brentp/slivar simple expressions to filter and annotate VCFs
• brentp/mosdepth fast coverage calculation from BAM
• NatPRoach/conduit reference-free transcriptome assembly
• papaemmelab/split_bed_by_index split a BAM file by estimated read counts.
• andreas-wilm/decontanimate Decontaminate FastQ files
• telatin/covtools various tools for coverage analysis
• ssocaller crossover calling from single-cell sperm BAM/CRAM