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bioinformatics_scripts

Some scripts to perform general bioinformatics functions

deepconsensus

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.

delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

deschrambler

easy_psmc_plot

this script is aim to plot the PSMC result by an easy way

extract_consensus_sequences_of_genes_from_bam_parallel

This is a series of scripts on the rapid construction of target interval consensus sequences from bam files and the rapid construction of phylogenetic trees as well as visualisations

hpa

Haplotype-based Phylogenetic Analysis for Polyploid

introblocker

The IntroBlocker ancestry inference algorithm

nphase

Ploidy agnostic phasing pipeline and algorithm

octopus

Bayesian haplotype-based mutation calling

populus_genomic_prediction_climate_vulnerability

shengxinzhuan.github.io

bioinfo

snp-sites

Finds SNP sites from a multi-FASTA alignment file

tgg

tomato graph pangenome

thex

Tree House Explorer (THEx) is a novel genome browser for exploring phylogenetic and genomic data in one succinct place.

transanno

accurate LiftOver tool for new genome assemblies

tree_utilities

Simulate gene trees given a newick species tree with branch lengths in coalescent units.

updog

Flexible Genotyping of Polyploids using Next Generation Sequencing Data

vcfpop

work_flow_of_population_genetics

整理常用的群体遗传学分析流程和脚本