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3krg-hap

Haplotype marker based on 3,000 Rice Genomes for subpopulation inference

alignmentconverters

Convert between common sequence alignment formats

alphafold

Open source code for AlphaFold.

anchorwave

sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation

assemblytics

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

asset-prev

assembly evaluation tool

augustus_train

Augustus Train pipline

badread

a long read simulator that can imitate many types of read problems

bamdst

a lightweight bam file depth statistical tool

betascan

Genome-wide scan for balancing selection using beta statistic

bsa

Bulked-Segregant Analysis using vcf file with or without parents

cactus

Official home of genome aligner based upon notion of Cactus graphs

canu

A single molecule sequence assembler for genomes large and small.

chatyuan

ChatYuan: Large Language Model for Dialogue in Chinese and English

chipseq

ChIP-seq peak-calling, QC and differential analysis pipeline.

cladepp

Code for running the CladePP phylogeentic profiling algorithm

contig2chr_byref

mapping contig to chr and link the contig to chr by mapping result

cutesv

Long read based human genomic structural variation detection with cuteSV

dbg

Naive de Bruijn graph implementation in python

dotplotly

Generate an interactive dot plot from mummer or minimap alignments

dspr-asm

Contains scripts and programs used to generate assemblies and variants for the DSPR project

edta

Extensive de-novo TE Annotator

flo

Same species annotation lift over pipeline.

gaap

A genome assembly assessment pipeline.

genblasta_to_gff

genepangenomebycollinearity

Pipeline to construct a gene-level pan genome with MCscan

genomescope

Fast genome analysis from unassembled short reads

genomesv

scripts uesed in SV analysis

gfa-spec

Graphical Fragment Assembly (GFA) Format Specification

ggheatmap

ggplot2 version of heatmap