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An open API service indexing awesome lists of open source software.
Projects in Awesome Lists by lh3
A curated list of projects in awesome lists by lh3 .
https://github.com/lh3/minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
bioinformatics genomics sequence-alignment spliced-alignment
Last synced: 01 Aug 2024
https://github.com/lh3/bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
bioinformatics fm-index genomics sequence-alignment
Last synced: 02 Aug 2024
https://github.com/lh3/seqtk
Toolkit for processing sequences in FASTA/Q formats
bioinformatics sequence-analysis
Last synced: 02 Aug 2024
https://github.com/lh3/bioawk
BWK awk modified for biological data
bioinformatics sequence-analysis
Last synced: 03 Aug 2024
https://github.com/lh3/minigraph
Sequence-to-graph mapper and graph generator
bioinformatics genome-graph genomics pan-genome sequence-alignment
Last synced: 01 Aug 2024
https://github.com/lh3/miniprot
Align proteins to genomes with splicing and frameshift
bioinformatics sequence-alignment
Last synced: 03 Aug 2024
https://github.com/lh3/miniasm
Ultrafast de novo assembly for long noisy reads (though having no consensus step)
bioinformatics denovo-assembly genomics
Last synced: 03 Aug 2024
https://github.com/lh3/gfatools
Tools for manipulating sequence graphs in the GFA and rGFA formats
bioinformatics genome-graph genomics
Last synced: 03 Aug 2024
https://github.com/lh3/biofast
Benchmarking programming languages/implementations for common tasks in Bioinformatics
Last synced: 03 Aug 2024
https://github.com/lh3/readfq
Fast multi-line FASTA/Q reader in several programming languages
bioinformatics sequence-analysis
Last synced: 03 Aug 2024
https://github.com/lh3/cgranges
A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)
algorithm bioinformatics genomics
Last synced: 03 Aug 2024
https://github.com/lh3/kmer-cnt
Code examples of fast and simple k-mer counters for tutorial purposes
bioinformatics genomics k-mer-counting
Last synced: 03 Aug 2024
https://github.com/lh3/psmc
Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
bioinformatics genomics population-genetics
Last synced: 03 Aug 2024
https://github.com/lh3/bedtk
A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
Last synced: 03 Aug 2024
https://github.com/lh3/ksw2
Global alignment and alignment extension
bioinformatics sequence-alignment
Last synced: 03 Aug 2024
https://github.com/lh3/fermikit
De novo assembly based variant calling pipeline for Illumina short reads
bioinformatics denovo-assembly genomics variant-calling
Last synced: 03 Aug 2024
https://github.com/lh3/minimap
This repo is DEPRECATED. Please use minimap2, the successor of minimap.
Last synced: 02 Aug 2024
https://github.com/lh3/hickit
TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
Last synced: 03 Aug 2024
https://github.com/lh3/bgt
Flexible genotype query among 30,000+ samples whole-genome
Last synced: 03 Aug 2024
https://github.com/lh3/dipcall
Reference-based variant calling pipeline for a pair of phased haplotype assemblies
Last synced: 03 Aug 2024