semi-reference-based short read compression
☆11Mar 5, 2019Updated 7 years ago
Alternatives and similar repositories for quark
Users that are interested in quark are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Improved multi-sample transcript abundance estimates using adaptive priors☆20Oct 29, 2018Updated 7 years ago
- Sequence Distance Graph framework: graph + reads + mapping + analysis☆25Jun 4, 2022Updated 3 years ago
- Computer simulator of multiplex tissue images from a set of user-defined parameters☆10Dec 13, 2022Updated 3 years ago
- The Dagstuhl Format for Assembly☆13Oct 16, 2017Updated 8 years ago
- ☆18Apr 10, 2015Updated 10 years ago
- nimble aligner that will map your reads to the references on a laptop☆11Jun 29, 2017Updated 8 years ago
- A pipeline to assess the quantification of transcripts.☆19Jun 6, 2022Updated 3 years ago
- An efficient index for the colored, compacted, de Bruijn graph☆111Mar 11, 2026Updated last week
- Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes☆31Jun 16, 2024Updated last year
- SAPLING: Suffix Array Piecewise Linear INdex for Genomics☆25Sep 1, 2020Updated 5 years ago
- Fast and compact locality-preserving minimal perfect hashing for k-mer sets.☆44Nov 18, 2023Updated 2 years ago
- in silico plasmid extraction☆13Sep 18, 2017Updated 8 years ago
- Bitpacked sequence trait and implementation☆16Feb 27, 2026Updated 3 weeks ago
- Finding putative exons and constructing splicegraphs using Trans-ABySS contigs☆11Nov 8, 2018Updated 7 years ago
- A hash map using the BooPHF perfect hash function☆13Sep 25, 2016Updated 9 years ago
- ☆57Aug 11, 2022Updated 3 years ago
- A fast constructor of the compressed de Bruijn graph from many genomes☆42Nov 27, 2025Updated 3 months ago
- Fast in-silico normalization algorithm for NGS data☆23Nov 1, 2021Updated 4 years ago
- Long read to reference genome mapping tool☆13Mar 14, 2024Updated 2 years ago
- Rapid sensitive and accurate read mapping via quasi-mapping☆90Jun 5, 2020Updated 5 years ago
- Identification of structural variations☆12Jul 22, 2022Updated 3 years ago
- This repo is deprecated. Please use gfatools instead.☆15Aug 17, 2018Updated 7 years ago
- ☆16Mar 15, 2026Updated last week
- A Python wrapper for the bbhash library for Minimal Perfect Hashing☆19Oct 26, 2025Updated 4 months ago
- De novo estimates of genetic relatedness from next-gen sequencing data☆45Jul 28, 2019Updated 6 years ago
- Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index☆86Mar 7, 2024Updated 2 years ago
- ☆16Jan 5, 2018Updated 8 years ago
- Building the compacted de Bruijn graph efficiently from references or reads.☆92Feb 26, 2026Updated 3 weeks ago
- Squeakr: An Exact and Approximate k -mer Counting System☆86Feb 23, 2025Updated last year
- Self-contained, multi-threaded fasta/q parser☆48Mar 10, 2026Updated last week
- Tools for working FASTQ files from sequencers (R1/R2/I1/I2)☆12Dec 6, 2024Updated last year
- de Bruijn CompAction in Low Memory☆23Jan 15, 2016Updated 10 years ago
- Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.☆22May 29, 2018Updated 7 years ago
- de Bruijn graph cOrrectiOn from graph aLignment☆11Jul 20, 2020Updated 5 years ago
- Fast & accurate alignment of barcoded short-reads☆32Jun 29, 2023Updated 2 years ago
- ☆24Apr 2, 2021Updated 4 years ago
- EXPERIMENTAL implementation of side graph☆10Apr 16, 2015Updated 10 years ago
- De novo genome assembler.☆11Jul 30, 2018Updated 7 years ago
- SIMD-parallel BLAST X-drop DP on sequence graphs☆24May 30, 2024Updated last year