| Deprecated tool description; use the IUC maintained tool description: https://toolshed.g2.bx.psu.edu/view/iuc/suite_khmer/cedc2ec71571
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 https://github.com/ged-lab/khmer and you can read the docs online here: http://khmer.readthedocs.org/ 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: Discussion http://lists.idyll.org/listinfo/khmer Announcements http://lists.idyll.org/listinfo/khmer-announce |
| 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 | |