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Gong216 (Gaorui Gong) / Starred · GitHub
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Catalogue of pairwise alignment algorithms and benchmarks

Rust 25 Updated Aug 7, 2024
C++ 31 5 Updated Feb 22, 2023

De novo assembly from Oxford Nanopore reads.

C++ 74 11 Updated Nov 13, 2024

Structural Variant Identification Method using Genome Assemblies

Python 93 11 Updated Sep 16, 2022

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

Python 12 2 Updated Nov 18, 2021

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.

Jupyter Notebook 16 6 Updated Oct 4, 2024

Detecting DNA methylation from PacBio CCS reads

Python 72 11 Updated Oct 31, 2024

Tandem repeat expansion detection or genotyping from long-read alignments

Python 69 8 Updated Sep 26, 2024

Allele-specific alignment sorting

Perl 53 20 Updated Jan 7, 2023

A minimap2 frontend for PacBio native data formats

Raku 176 27 Updated Oct 29, 2024

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

Python 63 4 Updated Jul 15, 2024

Pangenome-based genome inference

C++ 114 10 Updated Nov 8, 2024

PHAST

C 68 24 Updated Aug 29, 2023

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

R 58 6 Updated Oct 10, 2023

An updated pipeline for pangenome investigation

Python 269 34 Updated Oct 7, 2024

tomato graph pangenome

Python 73 18 Updated Dec 13, 2022

MCHelper: An automatic tool to curate transposable element libraries

Python 27 3 Updated Jun 23, 2024

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

C++ 9 1 Updated Apr 25, 2024

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

Rust 31 5 Updated Sep 11, 2024

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

Python 100 24 Updated Dec 11, 2023

Haplotypes phase-switching errors correction in long reads

Python 4 Updated May 6, 2024

Toolkit for calling structural variants using short or long reads

Cython 97 12 Updated Nov 15, 2024

Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation

Nextflow 81 8 Updated Nov 7, 2024

Creating alignment plots from bam files

Rust 56 1 Updated Nov 11, 2024

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

Python 368 44 Updated Dec 1, 2023
Roff 35 7 Updated Aug 14, 2019

Detecting multi-genome synteny using minimizer graph mapping

Python 71 1 Updated Oct 30, 2024
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