malonge's Stars
linsalrob/fastq-pair
Match up paired end fastq files quickly and efficiently.
SAMtoBAM/MUMandCo
MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (only v4) to detect Structural Variation
marbl/merqury
k-mer based assembly evaluation
volkansevim/alpha-CENTAURI
A python package from Pacific Biosciences to analyze centromeric sequences
marbl/Winnowmap
Long read / genome alignment software
thomasp85/patchwork
The Composer of ggplots
deeptools/HiCExplorer
HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
zlemmon/physalis-yellow-mapping
code for mapping the yellow flower mutant in Physalis pruinosa
mkirsche/Jasmine
Jasmine: SV Merging Across Samples
DaehwanKimLab/hisat2
Graph-based alignment (Hierarchical Graph FM index)
HajkD/LTRpred
De novo annotation of young retrotransposons
jmschrei/apricot
apricot implements submodular optimization for the purpose of selecting subsets of massive data sets to train machine learning models quickly. See the documentation page: https://apricot-select.readthedocs.io/en/latest/index.html
fritzsedlazeck/Sniffles
Structural variation caller using third generation sequencing
srividya22/geneLift
Gene model transfer from closely related reference genomes using cDNA alignments
bwa-mem2/bwa-mem2
The next version of bwa-mem
chanzuckerberg/shasta
[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads
MariaNattestad/Nchart
Creates an N-chart for comparing assembly lengths, including script for counting assembly lengths from a fasta file
lbcb-sci/racon
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
lh3/minigraph
Sequence-to-graph mapper and graph generator
jmschrei/pomegranate
Fast, flexible and easy to use probabilistic modelling in Python.
mkirsche/Iris
A module for improving the insertion sequences of structural variant calls
robbylewis7/Tastify
schatzlab/crossstitch
Code for phasing SVs with SNPs
pydata/numexpr
Fast numerical array expression evaluator for Python, NumPy, Pandas, PyTables and more
yangao07/TideHunter
TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain
deehzee/unionfind
A union-find disjoint sets data structure implemented in Python with the "Weighted Quick Union with Path Compression" algorithm.
human-pangenomics/hpgp-data
Data from the Human PanGenomics Project
VGP/vgp-assembly
VGP repository for the genome assembly working group
abyzovlab/CNVnator
a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
lh3/cgranges
A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)