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Repository khmer
Name: khmer
Owner: crusoe
Synopsis: In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
Deprecated tool description; use the IUC maintained tool description:

khmer is a library and suite of command line tools for working with DNA
sequence. It is primarily aimed at short-read sequencing data such as that
produced by the Illumina platform. khmer takes a k-mer-centric approach to
sequence analysis, hence the name.

The official repository is at
and you can read the docs online here:

There are two mailing lists dedicated to khmer, an announcements-only list
and a discussion list. To search their archives and sign-up for them, please
visit the following URLs:

Content homepage:
Type: unrestricted
Revision: 15:2c4635f5be47
This revision can be installed: True
Times cloned / installed: 29
Dependencies of this repository

Repository package_khmer_2_0 revision c7702a7d26e8 owned by crusoe

Contents of this repository

Name Description Version Minimum Galaxy Version
Trims fastq/fasta sequences at k-mers of a given abundance based on a provided k-mer countgraph. 2.0-5 any
Trims fastq/fasta sequences at k-mers with abundance below 50 based on a provided k-mer countgraph. 2.0-2 any
Count the median/avg k-mer abundance for each sequence in the input file, based on the k-mer counts in the given k-mer countgraph. Can be used to estimate expression levels (mRNAseq) or coverage (genomic/metagenomic). 2.0-1 any
Separate sequences that are annotated with partitions into grouped files. 2.0-2 any
Load, partition, and annotate FAST[AQ] sequences 2.0-3 any
Calculate abundance distribution of the k-mers in a given sequence file using a pre-made k-mer countgraph. 2.0-4 any
Filters a fastq/fasta file using digital normalization via median k-mer abundances. 2.0-4 any
Calculate abundance distribution of the k-mers in a given sequence file. 2.0-5 any

Assembly - Tools for working with assemblies
Next Gen Mappers - Tools for the analysis and handling of Next Gen sequencing data