Sequencing Tools

BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.

CryptoGenotyper is a bioinformatics tool for rapid Cryptosporidium identification. The CryptoGenotyper is a fast and reproducible tool that can be used to classify the genotype of Cryptosporidium samples by directly analyzing the DNA electropherogram files that correspond to two of its characteristic gene markers: SSU rRNA and gp60.

Peak finder for NGS datasets that can integrate replicates and assign peak boundaries accurately.

MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. Basically it is a ultra-fast alignment of large-scale DNA and protein sequences

OptiType is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles.

Aligns and optionally taxonomically classifies your rRNA gene sequences. Reference based multiple sequence alignment

Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.

A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.

Cluster a nucleotide dataset into representative sequences.

Tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.