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.

Kmc is a tool for efficient k-mer counting and filtering of reads based on k-mer content.

KmerGenie estimates the best k-mer length for genome de novo assembly.

KneadData is a tool designed to perform quality control on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments. In these experiments, samples are typically taken from a host in hopes of learning something about the microbial community on the host.

Kover is an out-of-core implementation of rule-based machine learning algorithms that has been tailored for genomic biomarker discovery.

Kraken2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer.

KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files.

Lambda is a local aligner optimized for many query sequences and searches in protein space.

LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator and is a classical molecular dynamics MD code.

LAPACK version 3.X is a comprehensive FORTRAN library that does linear algebra operations including matrix inversions, least squared solutions to linear sets of equations, eigenvector analysis, singular value decomposition, etc. It is a very comprehensive and reputable package that has found extensive use in the scientific community.

Last is used to find & align related regions of sequences.

pairwise DNA sequence aligner

Framework for running large collections of serial or multi-threaded applications.

LDhat is a package written in the C and C++ languages for the analysis of recombination rates from population genetic data.

LDJump is an R package to estimate variable recombination rates from population genetic data.

ldsc is a command line tool for estimating heritability and genetic correlation from GWAS summary statistics.

The learning module loads the prerequisites (such as anaconda and cudnn ) and makes ML applications visible to the user.

libflame is a portable library for dense matrix computations, providing much of the functionality present in LAPACK, developed by current and former members of the Science of High-Performance Computing SHPC group in the Institute for Computational Engineering and Sciences at The University of Texas at Austin. libflame includes a compatibility layer, lapack2flame, which includes a complete LAPACK implementation.

libFLAME AMD Optimized version is a portable library for dense matrix computations, providing much of the functionality present in Linear Algebra Package LAPACK. It includes a compatibility layer, FLAPACK, which includes complete LAPACK implementation.