My experimental tools on top of htslib. NOT OFFICIAL!!!
☆59Sep 11, 2025Updated 5 months ago
Alternatives and similar repositories for htsbox
Users that are interested in htsbox are comparing it to the libraries listed below
Sorting:
- your friendly pangenome graph genotyper☆10Feb 6, 2023Updated 3 years ago
- alignment to variation graph inducer☆157Updated this week
- base-level dotplots from PAF alignments☆32Sep 18, 2025Updated 5 months ago
- Naive PCA for genotype data☆10Jul 27, 2016Updated 9 years ago
- Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)☆49Sep 2, 2025Updated 6 months ago
- ProphAsm – a rapid computation of simplitigs directly from k-mer sets☆25Feb 17, 2023Updated 3 years ago
- nPoRe: n-Polymer Realigner for improved pileup-based variant calling☆18Jul 11, 2022Updated 3 years ago
- Analysis pipeline for functional metagenomic sequencing data obtained using nanopore sequencing☆12Nov 20, 2016Updated 9 years ago
- Processing WGS aDNA data using the ReichLab protocol☆13Mar 8, 2019Updated 6 years ago
- Dynamic time warping of Oxford Nanopore squiggle data to characterize tandem repeats.☆32Jul 2, 2020Updated 5 years ago
- Refinements of the WFA alignment algorithm with better complexity☆26Mar 31, 2022Updated 3 years ago
- Exact Tandem Repeat Finder (not a TRF replacement)☆51Oct 22, 2019Updated 6 years ago
- Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.☆46Jan 18, 2019Updated 7 years ago
- ☆14Aug 30, 2025Updated 6 months ago
- Iterative error correction of long reads☆13Dec 9, 2022Updated 3 years ago
- Archived version 1.0.2☆16Nov 25, 2019Updated 6 years ago
- Hidden Markov Model based Copy number caller☆20Dec 9, 2025Updated 2 months ago
- Sample Contamination Estimate from VCF☆20Nov 6, 2024Updated last year
- Error correction and variant calling algorithm for nanopore sequencing☆26Apr 23, 2016Updated 9 years ago
- DNA assembler developed on FER (Croatia), RBI (Croatia) and GIS (Singapore)☆18Jan 18, 2016Updated 10 years ago
- Proof-of-concept implementation of GWFA for sequence-to-graph alignment☆56May 29, 2024Updated last year
- mreps: software for tandem repeat identification in DNA☆15Nov 13, 2019Updated 6 years ago
- H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)☆73Oct 28, 2020Updated 5 years ago
- calling SVs from Blasr contig level alignments☆54Mar 9, 2018Updated 7 years ago
- TULIP - The Uncorrected Long read Itegration Pipeline☆27Jan 15, 2018Updated 8 years ago
- a pileup library that embraces the huge☆43Oct 2, 2020Updated 5 years ago
- Profile HMM-based hybrid error correction algorithm for long reads☆21Aug 15, 2018Updated 7 years ago
- ClaMSA (Classify Multiple Sequence Alignments).☆13Nov 21, 2024Updated last year
- DNN-based small variant caller☆12May 2, 2022Updated 3 years ago
- Layout module for raw de novo genome assembly of long uncorrected reads.☆21Feb 2, 2021Updated 5 years ago
- Toolkit for VNTR genotyping and repeat-pan genome graph construction☆31Aug 18, 2025Updated 6 months ago
- Scrooge is a high-performance pairwise sequence aligner based on the GenASM algorithm. Scrooge includes three novel algorithmic improveme…☆38Jun 23, 2023Updated 2 years ago
- Graph based multi genome aligner☆49Sep 17, 2021Updated 4 years ago
- ☆51Jun 25, 2024Updated last year
- recompute GFA link overlaps☆25Sep 14, 2022Updated 3 years ago
- Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs☆26Apr 29, 2024Updated last year
- Catalogue of pairwise alignment algorithms and benchmarks☆25Jan 6, 2026Updated last month
- Collection of utilities for working with PacBio-based assemblies☆13Apr 2, 2023Updated 2 years ago
- ☆16Jan 10, 2022Updated 4 years ago