uludag

fastq-dl

Download FASTQ files from SRA or ENA repositories.

taxopy

A Python package for obtaining complete lineages and the lowest common ancestor (LCA) from a set of taxonomic identifiers

blindschleiche

31 bioinformatics utilities in a trenchcoat

ViPTreeGen

a command line tool for viral proteomic tree generation, part of the ViPTree project: http://www.genome.jp/viptree

MAGRE

pyrodigal

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!

wildwood

Advanced random forest methods in Python

emgapi

MGnify RESTful API

kegg-pathways-completeness-tool

squirrel-sql-code

Share of the SQuirreL SQL source code originating from SourceForge, see https://squirrelsql.org

tomo-spectrum-matcher

A tool to normalize CryoET data by matching amplitude spectrums.

DeePiCt

Pipeline for the automatic detection and segmentation of particles and cellular structures in 3D Cryo-ET data, based on deep learning (convolutional neural networks).

mamba

The Fast Cross-Platform Package Manager

expresstest

00_Annotation_Pipeline

Annotation Pipeline for TrEMBL, UniProt, and KEGG

relion

Image-processing software for cryo-electron microscopy

ncov-ingest

A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV rebuilds.

SFS-coinfection-interactions

ArtiaX

ArtiaX is an open-source extension of the molecular visualisation program ChimeraX.

ChimeraX

Source code for molecular graphics program UCSF ChimeraX

ndstructs

Utility classes to deal with 5d arrays

edam-bioimaging

Ontology of bioimage informatics operations, topics, types of data, and data formats. EDAM-Bioimaging is an extension of the EDAM ontology (edamontology.org) dedicated to bioimaging data analysis, and developed in an open collaboration including partners from NEUBIAS (neubias.org), COMULIS (comulis.eu), and ELIXIR (elixir-europe.org)..

FROGS-wrappers

Galaxy wrappers for FROGS

FROGS

FROGS is a galaxy/CLI workflow designed to produce an OTUs count matrix from high depth sequencing amplicon data.

nf-needleall

A nextflow workflow for running needleall

nf-needleall-ava

ncbi-blast

Simple Python wrapper for NCBI Blast.

opengenomebrowser-tools

Set of scripts to aid OpenGenomeBrowser administrators import data

Affinity2Vec

Drug-target binding affinity prediction using representation learning, graph mining, and machine learning

BIGSdb

Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.