malonge's Stars
pyranges/pyranges
Performant Pythonic GenomicRanges
TGAC/KAT
The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.
wdecoster/NanoPlot
Plotting scripts for long read sequencing data
attractivechaos/klib
A standalone and lightweight C library
KamilSJaron/smudgeplot
Inference of ploidy and heterozygosity structure using whole genome sequencing data
mkirsche/Unitigging
Implementation of Unitigging Algorithm from "Toward Simplifying and Accurately Formulating Fragment Assembly (Myers et. al., 1995)
lh3/minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
dnbaker/dashing
Fast and accurate genomic distances using HyperLogLog
dnbaker/vec
Type-generic SIMD library for optimized generic code generation
cdarby/samovar
Somatic (mosaic) SNV caller for 10X Genomics data using random forest classification and feature-based filters
medvedevgroup/SibeliaZ
A fast whole-genome aligner based on de Bruijn graphs
lh3/fermikit
De novo assembly based variant calling pipeline for Illumina short reads
fbreitwieser/bamcov
:boom: Quickly calculate and visualize sequence coverage in alignment files
p2irc/deepplantphenomics
Deep learning for plant phenotyping.
gt1/daccord
d'accord is a non hybrid long read consensus program based on local de Bruijn graph assembly
bioinformatics-centre/AsmVar
A software for discovery, genotyping and characterization of structural variants
ruanjue/wtdbg2
Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
nanoporetech/flappie
Flip-flop basecaller for Oxford Nanopore reads
brentp/vcfanno
annotate a VCF with other VCFs/BEDs/tabixed files
oushujun/LTR_retriever
LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
ChristopherWilks/snaptron
fast webservices based query tool for large sets of genomic features
skovaka/UNCALLED
Raw nanopore signal mapper that enables real-time targeted sequencing
fritzsedlazeck/SURVIVOR_ant
A framework to annotate SVs with previous known SVs (vcf file) and or with genomic features (gff and or bed files)
rrwick/Bandage
a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
scikit-bio/scikit-bio
scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
thegenemyers/DAVIEWER
pb-jchin/FALCON_unzip
foo
PacificBiosciences/FALCON
FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries
thegenemyers/DALIGNER
Find all significant local alignments between reads
thegenemyers/DAZZ_DB
The Dazzler Data Base