k-SLAM

k-mer Sorted List Alignment and Metagenomics
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k-SLAM is a program for alignment based metagenomic analysis of large sets of high-throughput sequence data.
k-SLAM uses a k-mer based technique to rapidly find alignments between reads and genomes which are then validated using the Smith-Waterman algorithm.
Alignments are chained together into a pseudo-assembly to increase specificity.
Taxonomy is inferred using a Lowest Common Ancestor technique.
Output is presented as a Krona visualisation of per-read abundance.
Genes and variants are inferred from the alignments and output in SAM format.
k-SLAM is fast and highly parallelisable, with speeds of 5 million reads per minute on 150bp paired end data.

This web application is designed for classification of small datasets, larger files should be analysed using the full version of k-SLAM on the user's machine
This webserver uses the NCBI RefSeq bacterial, archaeal and viral genomes.
k-SLAM and this web application are offered for use as-is and without warranty.

Please cite
k-SLAM: Accurate and ultra-fast taxonomic classification and gene identification for large metagenomic datasets.
Ainsworth DJ, Sternberg MJE, Raczy C & Butcher A
Genome Biology (under review)