pirovc

genome_updater

Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

ganon

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more

multitax

Python package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)

metameta

grimer

GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and metadata with focus on contamination detection.

dudes

DUDes: a top-down taxonomic profiler for metagenomics and metaproteomics

taxsbp

TaxSBP - Taxonomic structured bin packing implementation

metabench

MetaBench is a pipeline to run and benchmark metagenomics tools. It covers database construction, taxonomic binning and profiling.

fgap

an automated gap closing tool

ganon_benchmark

benchmarking scripts for ganon

metametamerge

pylca

Lowest common ancestor (LCA) algorithm implementation in Python

.bashrc

My bashrc favorite confs

binpacking

Aims at optimal distribution of weighted items to bins (either a fixed number of bins or a fixed number of volume per bin). Data may be in form of list, dictionary, list of tuples or csv-file.

bioconda-recipes

Conda recipes for the bioconda channel.

ContamFilter

Implements NCBI Contamination Screen Publicly in CWL

cxxopts

Lightweight C++ command line option parser

DecontamManuscript

Reprocible analyses accompanying the paper introducing the decontam method

Frontiers_2017

Supplement for Frontiers article

grimer-reports

kmer_counting

Contains the source code for the new k-mer counting algorithm

lca

A Comparison Between Various Lowest Common Ancestor Algorithms

lca-1

Quick lowest-common-ancestor queries using sparse tables.

ncbi_data_growth

pirovc.github.io

readtools

rmq

Implementations of LCA and RMQ data structures from "The LCA Problem Revisited"

scikit-bio

scikit-bio is an open-source, BSD-licensed, Python package providing data structures, algorithms, and educational resources for bioinformatics.

seqan

SeqAn's official repository.

staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks