Purdue University

ISMapper searches for IS positions in sequence data using paired end Illumina short reads, an IS query/queries of interest and a reference genome. ISMapper reports the IS positions it has found in each isolate, relative to the provided reference genome.

IsoQuant is a tool for the genome-based analysis of long RNA reads, such as PacBio or Oxford Nanopores. IsoQuant allows to reconstruct and quantify transcript models with high precision and decent recall.

Scalable De Novo Isoform Discovery.

Ivar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

The Java Development Kit JDK released by Oracle Corporation in the form of a binary product aimed at Java developers. Includes a complete JRE plus tools for developing, debugging, and monitoring Java applications.

Jcvi is a collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.

The Julia programming language is a flexible dynamic language, appropriate for scientific and numerical computing, with performance comparable to traditional statically-typed languages.

Complete Jupyter Hub/Lab/Notebook environment.

Complete Jupyter Hub/Lab/Notebook environment.

Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence.

Kaiju is a tool for fast taxonomic classification of metagenomic sequencing reads using a protein reference database.

kakscalculator2 is a toolkit of incorporating gamma series methods and sliding window strategies.

Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.

UCSC command line bioinformatic utilities.

Keras is a deep learning API written in Python, running on top of the machine learning platform TensorFlow. It was developed with a focus on enabling fast experimentation.

Khmer is a tool for k-mer counting, filtering, and graph traversal FTW!

kissDE is a R package, similar to DEseq, but which works on pairs of variants, and tests if a variant is enriched in one condition. It has been developed to work easily with KisSplice output. It can also work with a simple table of counts obtained by any other means. It requires at least two replicates per condition and at least two conditions.

KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler that allows to identify SNPs, indels and alternative splicing events. It can deal with an arbitrary number of biological conditions, and will quantify each variant in each condition. It has been tested on Illumina datasets of up to 1G reads. Its memory consumption is around 5Gb for 100M reads.

KisSplice can also be used when a reference (annotated) genome is available, in order to annotate the variants found and help prioritize cases to validate experimentally. In this case, the results of KisSplice are mapped to the reference genome, using for instance STAR, and the mapping results are analysed using KisSplice2RefGenome.

KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.