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Quickly and accurately render even the largest data.
Visualize large time series data with plotly.py
Build data reports in 100% Python (a fork of Datapane)
Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output inc…
A bioinformatic toolkit to align genome assemblies into pangenome graphs
Common search engine for similarity based typing applications
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtool…
Embeddable genomic visualization component based on the Integrative Genomics Viewer
Fast and accurately polish the genome generated by long reads.
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
A tool to find sequencing data and metadata from public databases.
Finds SNP sites from a multi-FASTA alignment file
A tool for generating consensus long-read assemblies for bacterial genomes
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
k-mer based Pipeline to identify the Serotype from Illumina NGS reads
Utilities for building and managing bioconda recipes
Freezes a Flask application into a set of static files.
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
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)