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3d_dna_pipe

administrative-divisions-of-china

中华人民共和国行政区划：省级（省份）、 地级（城市）、 县级（区县）、 乡级（乡镇街道）、 村级（村委会居委会） ，**省市区镇村二级三级四级五级联动地址数据。

allele_frequencies

calculate allele frequencies from mpileup format

allelefinder

AlleleFinder is a tool for identifying allele genes from polyploid genome.

allhic_adjuster

Several scripts for adjusting ALLHiC assembly

annocomba

Automated genome annotation pipeline combining MAKER and funannotate with singularity and snakemake

annotation-workshop-2022

annotationpipeline-evm_based-dclab

Cantù Lab @ UC Davis - Annotation pipeline - EVM based

antimicrobial_peptide

Bioinformatics Institute project

armywormgenome

Code for the armymorm genome project https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13809

barrnap

:microscope: :leo: Bacterial ribosomal RNA predictor

bio-tools

record some useful bio tools

bioinfo_tools

TEs analysis

bioscripts

Collection of my bioinformatics scripts !

catfish-genome

Pipelines, code and ressources for creating a fully haplotype-resolved T2T assembly of the African catfish (Clarias gariepinus) combining PacBio HiFi, ONT long reads and Hi-C data.

chicken-t2t

Scripts that used in our chicken T2T manuscript.

chloranthus-sessilifolius-genome

learn

chloroplast-genome-assembly

A pipeline for assemble chroloplast genome using short/long reads

chloroplastannotation

Pipeline for Chloroplast annotation

chromosome_evolution_lepidoptera_ms

Scripts associated with 'Chromosome Evolution in Lepidoptera' manuscript

coral_genome_catalaphyllia_jardinei

csavanalysis

This analysis aims to detect convergent single amino acid variants among species from polyphyletic clades

denovote-eval

Supporting repository for article "Software Evaluation for 'de novo' Detection of Transposons"

dge_workshop_salmon_online

dotplotly

Generate an interactive dot plot from mummer or minimap alignments

easyspeciestree

Easily construct the ML species tree with single-copy gene shared by different species.

endhic

EndHic is a fast and easy-to-use Hi-C scaffolding tool, using the Hi-C links from contig end regions instead of whole contig regions to assemble large contigs into chromosomal-level scaffolds. EndHiC takes the HiC-pro's bin matrix results as input data.

evolutionary-rate

How to calculate dN/dS using PAML software

fast-plast

Automated de novo assembly of whole chloroplast genomes.

fasta_windows

A Rust implementation of sliding window stats over fastas.