Difference between revisions of "Kmer"

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Revision as of 00:52, 8 May 2012

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

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