Scripts to download genomes from the NCBI FTP servers

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets

open-source 3D scanning and processing pipeline

CLI tool for flexible and fast adaptive sampling on ONT sequencers

Surface velocity, object tracking, and river flow measurements in an open-source API

🐞 Convert NCBI taxonomy dump into lineages

Qiita - A multi-omics databasing effort

software for UCE (and general) phylogenomics

Python library to simulate evolutionary sequence data

PartitionFinder discovers optimal partitioning schemes for DNA sequences.

Basic Sequence Taxonomy Annotator

AMPtk: Amplicon ToolKit for NGS data (formally UFITS)

DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as well as insertions and deletions, from raw set(s) of reads.

A robust and fast clustering method for amplicon-based studies

eDNA metabarcoding pipeline

TaxonTableTools - A comprehensive, platform-independent graphical user interface software to explore and visualise DNA metabarcoding data

Guide to transcriptome assembly & analysis

Assign taxonomy with blast, can be used for qiime

Mitohelper: a mitochondrial reference sequence analysis tool for fish eDNA studies

Metabarcoding analyses pipeline - metaBarcoding and Environmental DNA Analysis Tool

NGSphy: phylogenomic simulation of next-generation sequencing data

NichePy: a collection of Python scripts for estimating overlap of ecological niche and species distribution models.

A utility to generate input files for taxonomy assignment in QIIME from the NCBI database