Purdue University

Abacas is a tool for algorithm based automatic contiguation of assembled sequences.

adaptive banded Partial Order Alignment

Abricate is a tool for mass screening of contigs for antimicrobial resistance or virulence genes.

ABySS is a de novo sequence assembler intended for short paired-end reads and genomes of all sizes.

Actc is used to align subreads to ccs reads.

AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.

Advntr is a tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data.

Afplot is a tool to plot allele frequencies in VCF files.

Afterqc is a tool for quality control of FASTQ data produced by HiSeq 2000/2500/3000/4000, Nextseq 500/550, MiniSeq, and Illumina 1.8 or newer.

Agat is a suite of tools to handle gene annotations in any GTF/GFF format.

AGFusion (pronounced 'A G Fusion') is a python package for annotating gene fusions from the human or mouse genomes.

Alfred is an efficient and versatile command-line application that computes multi-sample quality control metrics in a read-group aware manner.

Alien-hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs).

AlignStats produces various alignment, whole genome coverage, and capture coverage metrics for sequence alignment files in SAM, BAM, and CRAM format.

Allpathslg is a whole-genome shotgun assembler that can generate high-quality genome assemblies using short reads.

Alphafold is a protein structure prediction tool developed by DeepMind (Google). It uses a novel machine learning approach to predict 3D protein structures from primary sequences alone.

Amptk is a series of scripts to process NGS amplicon data using USEARCH and VSEARCH, it can also be used to process any NGS amplicon data and includes databases setup for analysis of fungal ITS, fungal LSU, bacterial 16S, and insect COI amplicons.

ANANSE is a computational approach to infer enhancer-based gene regulatory networks (GRNs) and to identify key transcription factors between two GRNs.

Anchorwave is used for sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation.

ANGSD is a software for analyzing next generation sequencing data.