A lightweight library for working with PAF (Pairwise mApping Format) files
☆31May 25, 2026Updated 4 months ago
Alternatives and similar repositories for pafpy
Users that are interested in pafpy are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Bam Read Index - Extract alignments from a bam file by readname☆29Apr 22, 2024Updated 2 years ago
- Functions to compare a SV call sets against a truth set.☆32Jun 18, 2025Updated last year
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆36Aug 4, 2021Updated 5 years ago
- Pangenome Graph Variation Format (PGVF)☆19Sep 24, 2020Updated 6 years ago
- Just a python fasta/q parser based on kseq.h☆14Jul 13, 2020Updated 6 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- GFA visualizer, GPU-accelerated using Vulkan☆80Aug 2, 2022Updated 4 years ago
- base-accurate DNA sequence alignments using WFA and mashmap3☆225Sep 28, 2026Updated 2 weeks ago
- A long read simulator based on badread idea☆23Oct 7, 2022Updated 4 years ago
- linearize and simplify variation graphs using blocked partial order alignment☆67Aug 21, 2026Updated last month
- the we-flyin WFA-guided ultralong tiling sequence aligner☆10May 13, 2021Updated 5 years ago
- ziglang + htslib☆22Oct 31, 2021Updated 4 years ago
- alignment to variation graph inducer☆165Jul 29, 2026Updated 2 months ago
- ☆11Dec 9, 2022Updated 3 years ago
- base-level dotplots from PAF alignments☆36Sep 18, 2025Updated last year
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Refinements of the WFA alignment algorithm with better complexity☆26Mar 31, 2022Updated 4 years ago
- R integration for edlib, a C/C++ library for pairwise sequence alignment using edit distance (Levenshtein distance).☆11Jul 20, 2025Updated last year
- A script to extract graph structure from multiple sequence alignment result and output as GFA/JSON for vg☆11Mar 27, 2019Updated 7 years ago
- A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)☆170May 28, 2024Updated 2 years ago
- ☆18Jan 29, 2025Updated last year
- ☆13Nov 15, 2017Updated 8 years ago
- Pipelines for using T2T genome as a reference☆15Dec 11, 2024Updated last year
- A repository for generating strobemers and evalaution☆79Apr 16, 2024Updated 2 years ago
- ProphAsm – a rapid computation of simplitigs directly from k-mer sets☆25Feb 17, 2023Updated 3 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Everything but the kitchen sink☆13Feb 6, 2025Updated last year
- R Bindings for htslib/bcf☆10Oct 4, 2023Updated 3 years ago
- ☆44Nov 20, 2021Updated 4 years ago
- RCK: Reconstruction of clone- and haplotype-specific Cancer Karyotypes☆19Apr 2, 2020Updated 6 years ago
- bioinformatics toolkit in rust☆109Aug 16, 2026Updated last month
- A fast K-mer counter for high-fidelity shotgun datasets☆149Jan 19, 2026Updated 8 months ago
- C implementation of the Landau-Vishkin algorithm☆36Apr 8, 2022Updated 4 years ago
- Rust crate with bindings and interface to the SPOA library for generating consensus sequences.☆13Apr 16, 2019Updated 7 years ago
- A command line program for large scale buffering between piped programs☆17Nov 19, 2021Updated 4 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- ☆14Sep 11, 2023Updated 3 years ago
- extract MSAs from genome variation graphs☆34Mar 24, 2026Updated 6 months ago
- Oxford Nanopore HDF/Fast5 to CRAM conversion tool☆22Dec 30, 2019Updated 6 years ago
- GFA insert into GenomicSQLite☆49Jun 7, 2021Updated 5 years ago
- A tool for de novo clustering of long transcriptomic reads☆14Oct 2, 2022Updated 4 years ago
- Genome browser hub for the T2T genomes and resources☆33Oct 1, 2026Updated last week
- Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes☆47Oct 13, 2024Updated 2 years ago