Kmer

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Description

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The kmer package is a suite of tools for DNA sequence analysis. It provides tools for searching (ESTs, mRNAs, sequencing reads); aligning (ESTs, mRNAs, whole genomes); and a variety of analyses based on kmers.

This also includes:

  • A2Amapper: ATAC, Assembly to Assembly Comparision tool:
    • Comparative mapping between two genome assemblies (same species), or between two different genomes (cross species).
  • Sim4db:
    • Spliced alignment of cDNA and genomic sequences, from the same (sim4) or related (sim4cc) species. Optimized for high-throughput batched alignment.
  • LEAFF:
    • LEAFF (ahem, Let's Extract Anything From Fasta) is a utility program for working with multi-fasta files. In addition to providing random access to the base level, it includes several analysis functions.
  • Meryl:
    • An out-of-core k-mer counter. The amount of sequence that can be processed for any size k depends only on the amount of free disk space.

Template:App Location ADD EXECUTABLE AND LIBRARY LOCATION DETAILS FOR INSTALLED VERSIONS OR REMOVE THIS MESSAGE

Running the application using modules

To use kmer with the environment modules system at HPC the following commands are available:

Get module information for kmer:

$module spider kmer

Load the default application module:

$module load kmer

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

  • HPC_KMER_DIR - directory where kmer is located.
  • HPC_KMER_BIN - executable directory
  • HPC_KMER_LIB - library directory
  • HPC_KMER_INCLUDE - include directory