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Gaorui Gong (Gong216)

Gong216

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pairwise-alignment

Catalogue of pairwise alignment algorithms and benchmarks

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VerityMap

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shasta

De novo assembly from Oxford Nanopore reads.

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svim-asm

Structural Variant Identification Method using Genome Assemblies

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Spermatogenesis

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callCodeml

This is used to call Codeml to calculate the positive selection of gene in Branch-Sites Model.(Require codon sequence)

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back_to_sequences

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SyntenyFinder

SyntenyFinder contains a collection of scripts to easily perform and visualize macrosynteny analysis when provided with the accessions of annotated chromosome-level genome assemblies from NCBI.

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ccsmeth

Detecting DNA methylation from PacBio CCS reads

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straglr

Tandem repeat expansion detection or genotyping from long-read alignments

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SNPsplit

Allele-specific alignment sorting

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pbmm2

A minimap2 frontend for PacBio native data formats

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pangenie

Pangenome-based genome inference

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ClipKIT

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

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phast

PHAST

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PATO

PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.

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panaroo

An updated pipeline for pangenome investigation

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TGG

tomato graph pangenome

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MCHelper

MCHelper: An automatic tool to curate transposable element libraries

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TGS-GapCloser2

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

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asgart

A genome-scale, fast, and precise segmental duplications mapping tool

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hapcorrect

Haplotypes phase-switching errors correction in long reads

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mummer2circos

Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments

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dysgu

Toolkit for calling structural variants using short or long reads

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egapx

Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation

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alignoth

Creating alignment plots from bam files

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bioconvert

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

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hypo-assembler

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ntSynt

Detecting multi-genome synteny using minimizer graph mapping

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hic_breakfinder

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