yananzh Goto Github PK

gsalign

GSAlign: an ultra-fast sequence alignment algorithm for intra-species genome comparison

gtdbtk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

helpful_commands

Command-line tools, commands, and code snippets for performing routine data processing and bioinformatics tasks

isescan

A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome

jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics

jupyterlab-desktop

JupyterLab desktop application, based on Electron.

learning-bioinformatics-at-home

resources for learning bioinformatics

linux-shell-scripting-cookbook-third-edition

Linux Shell Scripting Cookbook Third Edition, published by Packt

macsyfinder

MacSyFinder - Detection of macromolecular systems in protein datasets using systems modelling and similarity search.

macsyview

MacSyView - A web app for visualization of MacSyFinder's results.

mash

Fast genome and metagenome distance estimation using MinHash

mcorr

Inferring bacterial recombination rates from large-scale sequencing datasets.

mgefinder

A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.

microbeannotator

Pipeline for metabolic annotation of microbial genomes

mummer

Mummer alignment tool

oneliners

Useful bash one-liners for bioinformatics.

orthofinder

Phylogenetic orthology inference for comparative genomics

orthologr

Genome wide orthology inference and dNdS estimation

panaroo

An updated pipeline for pangenome investigation

pfb2019

Programming for Biology 2019

pgap

NCBI Prokaryotic Genome Annotation Pipeline

phandango

an interactive viewer for populations of bacterial genomes linked by a phylogeny

phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

phyml

PhyML -- Phylogenetic estimation using (Maximum) Likelihood

pilon

Pilon is an automated genome assembly improvement and variant detection tool

polypolish

a short-read polishing tool for long-read assemblies

poppunk

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

prokka

:zap: :aquarius: Rapid prokaryotic genome annotation

prokseq-v2.0

pyani

Application and Python module for average nucleotide identity analyses of microbes.