Veraqxb's Stars
Ming-Lian/NGS-analysis
二代测序数据分析
twbattaglia/RNAseq-workflow
A repository for setting up a RNAseq workflow
Starlitnightly/single_cell_tutorial
单细胞分析的中文pipeline
dvanoni/notero
A Zotero plugin for syncing items and notes into Notion
amkozlov/raxml-ng
RAxML Next Generation: faster, easier-to-use and more flexible
GSLBiotech/mafft
Align multiple amino acid or nucleotide sequences.
millanek/Dsuite
Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species
erdogant/pca
pca: A Python Package for Principal Component Analysis.
alexdobin/STAR
RNA-seq aligner
broadinstitute/gatk
Official code repository for GATK versions 4 and up
arq5x/bedtools2
bedtools - the swiss army knife for genome arithmetic
leventov/Koloboke
Java Collections till the last breadcrumb of memory and performance
songlab-cal/gpn
Genomic Pre-trained Network
signalbash/how_are_we_stranded_here
Check strandedness of RNA-Seq fastq files
linzhi2013/MitoZ
MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes
hwc2021/GSAT
Graph-based Sequence Assembly Toolkit
sanger-pathogens/circlator
A tool to circularize genome assemblies
oushujun/EDTA
Extensive de-novo TE Annotator
wyp1125/MCScanX
MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
simonhmartin/genomics_general
General tools for genomic analyses.
lh3/minigraph
Sequence-to-graph mapper and graph generator
kage-genotyper/kage
Alignment-free genotyper for SNPs and short indels, implemented in Python.
LeanQ/SPLITREADER
Split-read pipeline for the identification of non-reference TE insertions with TSDs
pkalbers/geva
Genealogical Estimation of Variant Age (GEVA)
HajkD/LTRpred
De novo annotation of young retrotransposons
shuyuzheng/Chloroplot
A R tool to parse and visualize chloroplast genomes
broadinstitute/picard
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
lh3/bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
DaehwanKimLab/hisat2
Graph-based alignment (Hierarchical Graph FM index)
Kinggerm/GetOrganelle
Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)