malonge's Stars
shenwei356/kmcp
Accurate metagenomic profiling && Fast large-scale sequence/genome searching
schneebergerlab/plotsr
Tool to plot synteny and structural rearrangements between genomes
marbl/verkko
Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.
amplab/snap
Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
tjiangHIT/cuteSV
Long read based human genomic structural variation detection with cuteSV
eldariont/svim
Structural Variant Identification Method using Long Reads
dfguan/pin_hic
A Hi-C scaffolding method
nanoporetech/bonito
A PyTorch Basecaller for Oxford Nanopore Reads
kjenike/HetTrek
LiLabAtVT/DeepTE
Neural network classification of TE
harta55/EnTAP
Eukaryotic Non-Model Transcriptome Annotation Pipeline - Latest Release v1.3.0 - HGT Analysis Released! Revamped figures/graphics coming soon.
suchow/Dissertate
Beautiful LaTeX dissertation templates.
baoxingsong/AnchorWave
Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation
kullrich/dagchainer
Fork of the DAGchainer project https://sourceforge.net/projects/dagchainer
idanefroni/Conservatory
Identification of conserved non-coding sequences in plants
ydLiu-HIT/SKSV
ultrafast structural variation detection from circular consensus sequencing reads
cpockrandt/genmap
GenMap - Fast and Exact Computation of Genome Mappability
haowenz/chromap
Fast alignment and preprocessing of chromatin profiles
gamcil/clinker
Gene cluster comparison figure generator
schneebergerlab/syri
Synteny and Rearrangement Identifier
davidemms/OrthoFinder
Phylogenetic orthology inference for comparative genomics
lbcb-sci/raven
De novo genome assembler for long uncorrected reads
arq5x/grabix
a wee tool for random access into BGZF files.
brentp/cyvcf2
cython + htslib == fast VCF and BCF processing
hdashnow/TandemRepeatFinder_scripts
lh3/unimap
A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment
bihealth/vcfpy
Python 3 library with good support for both reading and writing VCF
NBISweden/AGAT
Another Gtf/Gff Analysis Toolkit
marbl/CHM13-issues
CHM13 human reference genome issue tracking
huangnengCSU/BlockPolish
BlockPolish: accurate polishing of long-read assembly via block divide-and-conquer