mcshane's Stars
google/deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
tanghaibao/jcvi
Python library to facilitate genome assembly, annotation, and comparative genomics
fenderglass/Flye
De novo assembler for single molecule sequencing reads using repeat graphs
rrwick/Bandage
a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
rrwick/Unicycler
hybrid assembly pipeline for bacterial genomes
ablab/quast
Genome assembly evaluation tool
nanopore-wgs-consortium/NA12878
Data and analysis for NA12878 genome on nanopore
rrwick/Basecalling-comparison
A comparison of different Oxford Nanopore basecallers
fulcrumgenomics/fgbio
Tools for working with genomic and high throughput sequencing data.
luntergroup/octopus
Bayesian haplotype-based mutation calling
arq5x/poretools
a toolkit for working with Oxford nanopore data
walaj/svaba
Structural variation and indel detection by local assembly
roblanf/minion_qc
Quality control for MinION sequencing data
vibansal/HapCUT2
software tools for haplotype assembly from sequence data
marbl/SALSA
SALSA: A tool to scaffold long read assemblies with Hi-C data
PitchInteractiveInc/Phinch
Phinch is an open-source framework for visualizing biological data, funded by a grant from the Alfred P. Sloan foundation. This project represents an interdisciplinary collaboration between Pitch Interactive, a data visualization studio in Oakland, CA, and biological researchers at UC Riverside.
verilylifesciences/genomewarp
GenomeWarp translates genetic variants from one genome assembly version to another.
schloi/MARVEL
The MARVEL assembler
HingeAssembler/HINGE
Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution"
jltsiren/gbwt
Substring index for paths in a graph
mklarqvist/tomahawk
Fast calculations of linkage-disequilibrium in large-scale human cohorts
jkbonfield/crumble
Exploration of controlled loss of quality values for compressing CRAM files
TGAC/NanoOK
Analysis tool for Nanopore sequencing data
PacificBiosciences/apps-scripts
Miscellaneous scripts for applications of PacBio systems
wtsi-hpag/Scaff10X
Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads
mw55309/poRe_docs
bcgsc/arks
ARCHIVED 🌈Alignment-free scaffolding of genome assemblies with 10x Genomics Chromium reads. ARCS/ARKS projects have been consolidated: https://github.com/bcgsc/arcs
pd3/bxcheck
Toolset for QC and processing 10x genomics data
simpsonlab/preqclr
preqclr is a software tool that reports on quality for long read sequencing data without the use of a reference genome.
skoren/NanoGrid
Nanopolish wrapper for SGE