Bioinformatics Tools

A tool that finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.

COSG is a cosine similarity-based method for more accurate and scalable marker gene identification.

ABACAS is intended to rapidly contiguate (align, order, orientate) , visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. It uses MUMmer to find alignment positions and identify syntenies of assembly contigs against the reference. The output is then processed to generate a pseudomolecule taking overlaping contigs and gaps in to account. MUMmer's alignment generating programs, Nucmer and Promer are used followed by the 'delta-filter' utility function. Users could also run tblastx on contigs that are not used to generate the pseudomolecule.

Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.

abPOA: an SIMD-based C library for fast partial order alignment using adaptive band. abPOA can perform multiple sequence alignment (MSA) on a set of input sequences and generate a consensus sequence by applying the heaviest bundling algorithm to the final alignment graph.

ACTC (Align subreads to CCS reads) is developed by Pacific Biosciences and provides a one-click solution for aligning individual subreads to the corresponding circular consensus (CCS) reads — useful in workflows involving HiFi/CCS read analysis from PacBio sequencing.

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.

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC results of each fastq file/pair.

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

BAM Statistics, Feature Counting and Annotation

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. It can handle Ion Torrent, MiSeq, and 454 data.

Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

Sinto is a toolkit for processing aligned single-cell data.