CAShuangchao

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vg

tools for working with genome variation graphs

Language:C++NOASSERTION1097 48 2051

jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics

Language:PythonBSD-2-Clause743 36 477

OrthoFinder

Phylogenetic orthology inference for comparative genomics

Language:PythonGPL-3.0684 27 894

cdhit

Automatically exported from code.google.com/p/cdhit

Language:PerlGPL-2.0635 28 133

Sniffles

Structural variation caller using third generation sequencing

Language:PythonNOASSERTION548 26 477

Liftoff

An accurate GFF3/GTF lift over pipeline

Language:PythonGPL-3.0427 7 155

minigraph

Sequence-to-graph mapper and graph generator

Language:CMIT410 29 109

BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes

Language:PerlNOASSERTION352 21 790

syri

Synteny and Rearrangement Identifier

Language:CythonMIT323 6 255

SnpEff

Language:JavaNOASSERTION247 26 503

Jasmine

Jasmine: SV Merging Across Samples

Language:JavaMIT178 10 58

TGS-GapCloser

A gap-closing software tool that uses long reads to enhance genome assembly.

Language:C++GPL-3.0171 7 79

svim

Structural Variant Identification Method using Long Reads

Language:PythonGPL-3.0152 6 71

seqwish

alignment to variation graph inducer

Language:C++MIT143 14 65

GALBA

GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the scenario where high quality proteins from one or several closely related species are available.

Language:PerlNOASSERTION127 10 33

pbsv

pbsv - PacBio structural variant (SV) calling and analysis tools

Language:PythonBSD-3-Clause-Clear126 190

svim-asm

Structural Variant Identification Method using Genome Assemblies

Language:PythonGPL-3.092 5 27

TEsorter

TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes

Language:Pep8GPL-3.087 7 53

NAM-genomes

Detailed bioinformatics scripts and methods used in the NAM genome paper.

Language:RMIT71 15 6

geta

Language:PerlGPL-3.067 5 36

NLR-Annotator

NLR-Annotator upload

Language:JavaGPL-3.056 7 34

smrtsv2

Structural variant caller

Language:PythonMIT53 3 57

NovoGraph

NovoGraph: building whole genome graphs from long-read-based de novo assemblies

Language:PerlMIT44 15 25

Picky

Structural Variants Pipeline for Long Reads

Language:PerlNOASSERTION44 10 14

LINKVIEW2

DNA序列比对结果可视化展示工具

Language:TypeScript42 3 4

NanoVar

Structural variant caller for low-depth long-read sequencing data

Language:PythonGPL-3.021 10

gnx-tools

genome basic statistics tool (e.g. n50, n10, ng50,...)

Language:Java14 40

TGSRICEPAN

The codes of "the Third Generation Sequencing of 111 rice genomes reveals a huge size of novel genome sequence in the RICE PAN-genome"

Language:Python8 3 2

RiceNavi

Language:Perl500

NWRGenomeAssembly_v1.0

Language:sed100