Purdue University

ASGAL (Alternative Splicing Graph ALigner) is a tool for detecting the alternative splicing events expressed in a RNA-Seq sample with respect to a gene annotation.

Aspera Connect is software that allows download and upload data. The software includes a command line tool (ascp) that allows scripted data transfer.

Assembly-stats is a tool to get assembly statistics from FASTA and FASTQ files.

The ENCODE ATAC-seq pipeline is used for quality control and statistical signal processing of short-read sequencing data, producing alignments and measures of enrichment. It was developed by Anshul Kundaje's lab at Stanford University.

Ataqv is a toolkit for measuring and comparing ATAC-seq results, made in the Parker lab at the University of Michigan.

aTRAM (automated target restricted assembly method) is an iterative assembler that performs reference-guided local de novo assemblies using a variety of available methods.

Atropos is a tool for specific, sensitive, and speedy trimming of NGS reads.

Augur is the bioinformatics toolkit we use to track evolution from sequence and serological data.

AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.

The AutoDock Suite is a growing collection of methods for computational docking and virtual screening, for use in structure-based drug discovery and exploration of the basic mechanisms of biomolecular structure and function.

The AWS Command Line Interface CLI is a unified tool to manage your AWS services from command line.

Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is to process your data with a broad set of tools, so that you can get to the fun part of analyses quicker!<

Bali-phy is a tool for bayesian co-estimation of phylogenies and multiple alignments via MCMC.

Bam-readcount is a utility that runs on a BAM or CRAM file and generates low-level information about sequencing data at specific nucleotide positions.

Bamgineer is a tool that can be used to introduce user-defined haplotype-phased allele-specific copy number variations (CNV) into an existing Binary Alignment Mapping (BAM) file with demonstrated applicability to simulate somatic cancer CNVs in phased whole-genome sequencing datasets.

Bamliquidator is a set of tools for analyzing the density of short DNA sequence read alignments in the BAM file format.

Bamsurgeon are tools for adding mutations to .bam files, used for testing mutation callers.

BamTools is a programmer API and an end-user toolkit for handling BAM files. This container provides a toolkit-only version (no API to build against).

Bamutil is a collection of programs for working on SAM/BAM files.

Barrnap: BAsic Rapid Ribosomal RNA Predictor.