Difference between revisions of "Kmer"

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*Meryl:
 
*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.  
 
** 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.  
 
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==Required Modules==
 
==Required Modules==
 
[[Modules|modules documentation]]
 
[[Modules|modules documentation]]
 
===Serial===
 
===Serial===
 
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==System Variables==
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
*HPC_KMER_BIN - executable directory
 
*HPC_KMER_BIN - executable directory
 
*HPC_KMER_LIB - library directory
 
*HPC_KMER_LIB - library directory
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WRITE CITATION HERE
 
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=Validation=
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* Validated 4/5/2018

Latest revision as of 21:21, 6 December 2019

Description

kmer website  

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.

Required Modules

modules documentation

Serial

  • kmer

System Variables

  • HPC_KMER_DIR - installation directory
  • HPC_KMER_BIN - executable directory
  • HPC_KMER_LIB - library directory
  • HPC_KMER_INCLUDE - include directory




Validation

  • Validated 4/5/2018