malonge's Stars
PengNi/deepsignal-plant
Detecting methylation using signal-level features from Nanopore sequencing reads of plants
oushujun/EDTA
Extensive de-novo TE Annotator
deeptools/pyBigWig
A python extension for quick access to bigWig and bigBed files
morispi/CONSENT
Scalable long read self-correction and assembly polishing with multiple sequence alignment
shenwei356/seqkit
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
eldariont/svim-asm
Structural Variant Identification Method using Genome Assemblies
ChaissonLab/LRA
Long read aligner
pkerpedjiev/nometoexecutor
urmi-21/orfipy
Fast and flexible ORF finder
jmschrei/ledidi
Ledidi turns any machine learning model into a biological sequence editor, allowing you to design sequences with desired properties.
ArimaGenomics/mapping_pipeline
Mapping pipeline for data generated using Arima-HiC
ryanlayer/samplot
Plot structural variant signals from many BAMs and CRAMs
lh3/gfatools
Tools for manipulating sequence graphs in the GFA and rGFA formats
tanghaibao/jcvi
Python library to facilitate genome assembly, annotation, and comparative genomics
lh3/dipcall
Reference-based variant calling pipeline for a pair of phased haplotype assemblies
pangenome/pggb
the pangenome graph builder
arangrhie/merfin
Evaluate variant calls and its combination with k-mer multiplicity
compbiol/CAMSA
CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies
marcelauliano/MitoHiFi
Find, circularise and annotate mitogenome from PacBio assemblies
Martinsos/edlib
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
rrwick/Minipolish
A tool for Racon polishing of miniasm assemblies
COMBINE-lab/pufferfish
An efficient index for the colored, compacted, de Bruijn graph
chhylp123/hifiasm
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
TriticumAestivum/Assembly
This repository lists the location of the Triticum aestivum 4.0 assembly.
TriticumAestivum/Annotation
This repository contains the full set of genes for Triticum aestivum including protein-coding and noncoding genes.
higlass/higlass
Fast, flexible and extensible genome browser.
open2c/cooler
A cool place to store your Hi-C
Cibiv/IQ-TREE
Efficient phylogenomic software by maximum likelihood
lh3/yak
Yet another k-mer analyzer
maickrau/tangle-resolution