Reorients assembled microbial sequences

A collection of resources for learning about tools and programming languages related to Bioinformatics

Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023

This repo collects the list of learning online resources related to microbiome computational science and tools.

resources for learning bioinformatics

⚡ Dynamically generated stats for your github readmes

An accurate GFF3/GTF lift over pipeline

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

Compute a pairwise SNP distance matrix from one or two alignment(s)

BEAV: Bacterial Element Annotation reVamped

🔎 💊 Mass screening of contigs for antimicrobial and virulence genes

API Documentation Browser

Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]

SplitsTree App

COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)

BItsliced Genomic Signature Index - Efficient indexing and search in very large collections of WGS data

BItsliced Genomic Signature Index - Efficient indexing and search in very large collections of WGS data

Accelerated BLAST compatible local sequence aligner.

GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click the first link to launch: https://achtman-lab.github.io/Gra…

List of Computer Science courses with video lectures.

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

Global alignment and alignment extension

Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Antimicrobial Resistance Identification By Assembly

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

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

A tool to circularize genome assemblies

PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)