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Mass screening of contigs for antibiotic resistance genes

Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets.

adxv can be used to display and analyze 2-D area detector data. It is optimized to display X-Ray crystallography diffraction images.

Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.

ALBULA is DECTRIS’ dedicated software for display and analysis of image data from PILATUS and EIGER detectors

Trimmer of contaminant oligonucleotide sequences such as primers and adapters

This package provides an implementation of the inference pipeline of AlphaFold v2.3.2

ANGSD: Analysis of next generation Sequencing Data

An annotated data matrix

antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell

A platform for integrated multi-omics

The container system for secure high performance computing

Scaffolding genome sequence assemblies using 10X Genomics data

aria2 is a lightweight multi-protocol & multi-source, cross platform download utility operated in command-line. It supports HTTP/HTTPS, FTP, SFTP, BitTorrent and Metalink.

Cancer Genome Projects workflow implementation of the ASCAT copy number algorithm for paired end sequencing.

IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera tools for performing high-speed, secure data transfers from the command line.

analyze a genome assembly by comparing it to a reference genome

ATLAS stands for Analysis Tools for Low-coverage and Ancient Samples. These tools cover all programs necessary to obtain variant calls, estimates of heterozygosity and more from a BAM file. There are sequence data processing tools, diagnostic tools, and variant discovery tools, similar to GATK by the Broad Institute.

AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments.

Includes

Universal Command Line Interface for Amazon Web Services

AxonDeepSeg is an open-source software using deep learning and aiming at automatically segmenting axons and myelin sheaths from microscopy images. It performs 3-class semantic segmentation using a convolutional neural network.