malonge's Stars
esolares/HapSolo
Reduction of Althaps and Duplicate Contigs for Improved Hi-C Scaffolding
ekg/seqwish
alignment to variation graph inducer
sanger-tol/PretextView
OpenGL Powered Pretext Contact Map Viewer
LeanQ/SPLITREADER
Split-read pipeline for the identification of non-reference TE insertions with TSDs
mahulchak/svmu
A program to call variants from genome alignment
medvedevgroup/BubbZ
arangrhie/T2T-Polish
Evaluation and polishing workflows for T2T genome assemblies
mkirsche/Grafter
Scaffolding with Ultralong Reads
bioconda/bioconda-recipes
Conda recipes for the bioconda channel.
ablab/TandemTools
Tool for assessing/improving assembly quality in extra-long tandem repeats
lh3/hickit
TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
alekseyzimin/masurca
marbl/CHM13
The complete sequence of a human genome
maickrau/GraphAligner
Nextomics/NextPolish
Fast and accurately polish the genome generated by long reads.
igvteam/igv.js
Embeddable genomic visualization component based on the Integrative Genomics Viewer
marbl/SALSA
SALSA: A tool to scaffold long read assemblies with Hi-C data
dfguan/purge_dups
haplotypic duplication identification tool
marbl/canu
A single molecule sequence assembler for genomes large and small.
mamba-org/mamba
The Fast Cross-Platform Package Manager
mschatz/genometools
Collection of smaller utilities and helper scripts
gpertea/gffread
GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
univieCUBE/gepard
Genome Pair Rapid Dotter
lh3/calN50
Compute N50/NG50 and auN/auNG
mkirsche/vcfigv
Code for generating IGV screenshots from VCF files
nanoporetech/megalodon
Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.
samtools/samtools
Tools (written in C using htslib) for manipulating next-generation sequencing data
lh3/kmer-cnt
Code examples of fast and simple k-mer counters for tutorial purposes
martinus/robin-hood-hashing
Fast & memory efficient hashtable based on robin hood hashing for C++11/14/17/20
agshumate/Liftoff
An accurate GFF3/GTF lift over pipeline