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).
- Spliced alignment of cDNA and genomic sequences, from the same (sim4) or related (sim4cc) species. Optimized for high-throughput batched alignment.
- 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.
- 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.
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