SAPLING: Suffix Array Piecewise Linear INdex for Genomics
☆25Sep 1, 2020Updated 5 years ago
Alternatives and similar repositories for sapling
Users that are interested in sapling are comparing it to the libraries listed below
Sorting:
- a toolset for efficient analysis of 10X Genomics linked read data sets, in particular for de novo assembly☆15Nov 27, 2019Updated 6 years ago
- Johns Hopkins University student-led genomics paper discussion group☆13Apr 19, 2020Updated 5 years ago
- ☆10Jun 9, 2020Updated 5 years ago
- SeqOthello supports fast coverage query and containment query.☆12May 8, 2019Updated 6 years ago
- semi-reference-based short read compression☆11Mar 5, 2019Updated 6 years ago
- ☆14Jan 31, 2020Updated 6 years ago
- nimble aligner that will map your reads to the references on a laptop☆11Jun 29, 2017Updated 8 years ago
- ☆16Feb 5, 2026Updated 3 weeks ago
- Implicit Interval Tree with Interpolation Index☆42Jul 13, 2022Updated 3 years ago
- Fast and compact locality-preserving minimal perfect hashing for k-mer sets.☆43Nov 18, 2023Updated 2 years ago
- ☆15Apr 6, 2016Updated 9 years ago
- Portable Crystal binary distributions for Linux on x86_64☆15Mar 22, 2021Updated 4 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
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Aug 4, 2021Updated 4 years ago
- Practical Dynamic de Bruijn Graphs☆18Oct 1, 2020Updated 5 years ago
- a long-read error correction tool using the multi-string Burrows Wheeler Transform☆45Jul 7, 2020Updated 5 years ago
- FMSI is a highly memory efficient exact k-mer set index based on masked superstrings and the masked Burrows-Wheeler transform☆23Nov 20, 2025Updated 3 months ago
- A tool to detect structural variant☆17Mar 27, 2023Updated 2 years ago
- De Bruijn graph representation in low memory☆35Jul 6, 2024Updated last year
- A fast, AVX2 and ARM Neon accelerated FM index library☆36Dec 9, 2024Updated last year
- GCLib - Genomic C++ library of reusable code for bioinformatics projects☆39Jul 12, 2025Updated 7 months ago
- Combined clonality and transcriptome scRNAseq clustering method☆11Dec 3, 2022Updated 3 years ago
- Sensitive and Fast Alignment Search Tool for Long Read sequencing Data.☆40Jul 15, 2019Updated 6 years ago
- Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.☆24Jan 9, 2021Updated 5 years ago
- Improved multi-sample transcript abundance estimates using adaptive priors☆20Oct 29, 2018Updated 7 years ago
- A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment☆87Apr 8, 2021Updated 4 years ago
- A hash map using the BooPHF perfect hash function☆13Sep 25, 2016Updated 9 years ago
- R Package for phasing of single cell Strand-seq data☆10Jan 14, 2025Updated last year
- Run-length compressed BWT with LZ77 sampled suffix array☆10Apr 25, 2022Updated 3 years ago
- Generate HTML report for a set of genomic regions or DESeq2/edgeR results☆10Jan 14, 2025Updated last year
- Analysis tool for NG-Capture-C, Tri-C and Tiled-C data☆10Oct 13, 2025Updated 4 months ago
- K-means clustering for large single-cell datasets☆12Feb 10, 2026Updated 2 weeks ago
- Implementation of eBWT using Prefix-free parse (PFP)☆14Jul 14, 2025Updated 7 months ago
- Negative binomial regression for Spatial Transcriptomics data as described in Maaskola et al. 2018☆22Nov 2, 2018Updated 7 years ago
- Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs☆26Apr 29, 2024Updated last year
- Fast in-silico normalization algorithm for NGS data☆23Nov 1, 2021Updated 4 years ago
- A fast constructor of the compressed de Bruijn graph from many genomes☆42Nov 27, 2025Updated 3 months ago
- Clinical Variant Annotation Pipeline☆10Apr 21, 2020Updated 5 years ago
- CNV calling algorithm for detection of homozygous and hemizygous deletions from whole exome sequencing data☆12Nov 9, 2025Updated 3 months ago