brentp / hts-nim
nim wrapper for htslib for parsing genomics data files
☆155Updated 2 months ago
Related projects ⓘ
Alternatives and complementary repositories for hts-nim
- useful command-line tools written to showcase hts-nim☆49Updated 4 years ago
- Nim Library for sequence (protein/nucleotide) bioinformatics☆22Updated 4 years ago
- command-line querying+conversion of bigwigs and a nim wrapper for dpryan's libbigwig☆16Updated 4 years ago
- fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"☆270Updated 9 months ago
- genetic variant expressions, annotation, and filtering for great good.☆252Updated 5 months ago
- fast easy interval overlapping for nim-lang☆26Updated 3 years ago
- find large indels (in the blind spot between GATK/freebayes and SV callers)☆39Updated 6 years ago
- Detect novel (and reference) STR expansions from short-read data☆62Updated last year
- Experimental getopt, gzip reader, FASTA/Q parser and interval queries in nim-lang☆32Updated 4 years ago
- use the noise☆15Updated 4 years ago
- igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"☆122Updated last year
- seqcover allows users to view coverage for hundreds of genes and dozens of samples☆50Updated 3 years ago
- Annotate non-coding regulatory vars using our GREEN-DB, prediction scores, conservation and pop AF☆18Updated 2 months ago
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆702Updated 2 months ago
- A wrapper to Heng Li's kseq/readfq, an efficient FastQ/Fasta parser☆15Updated last year
- Fast fusion detection using kallisto☆80Updated last month
- DNA kmer operations for nim☆14Updated 2 years ago
- Yet Another Chimeric Read Detector☆72Updated 2 weeks ago
- RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference…☆65Updated 2 years ago
- The D4 Quantitative Data Format☆158Updated last month
- Squeakr: An Exact and Approximate k -mer Counting System☆85Updated 9 months ago
- SQL-like query language for the SAM/BAM file format☆26Updated last year
- FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds☆74Updated 4 years ago
- Assembly Based ReAligner☆72Updated 6 years ago
- Genotype and phase short tandem repeats using Illumina whole-genome sequencing data☆95Updated last year
- LoFreq Version 3☆27Updated 3 years ago
- don't get DUP'ed or DEL'ed by your putative SVs.☆101Updated 3 years ago
- Basic, no assumptions, multi-pileup☆24Updated 10 years ago
- MetaSV: An accurate and integrative structural-variant caller for next generation sequencing☆54Updated 7 years ago
- Bayesian genotyper for structural variants☆126Updated 3 years ago