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Assemble Reads with MEGAHIT v1.2.9
MEGAHIT

v.2.4.2

Launch

Assemble metagenomic reads using the MEGAHIT assembler.

This is a KBase wrapper for the ultra-fast and memory-efficient metagenome assembler MEGAHIT. MEGAHIT is a single node assembler optimized for large and complex metagenomics next-generation sequencing (NGS) reads, such as soil. It can also be used to assemble reads from less complex metagenomes. It makes use of succinct de Bruijn graphs (SdBG) to achieve a low memory assembly. The output is an assembly object, which can be used for downstream analysis such as binning genomes from a metagenome assembly.

MEGAHIT uses a multiple k-mer strategy. Minimum k-mer size, maximum k-mer size, and the k-mer step size for each iteration can be set in the parameters. Values for k must be odd numbers while the step size must be an even number.

User feedback and extensive use on KBase has led to these observations about setting input parameters for MEGAHIT:

KBase module authors:

KBase module authors:

Related Publications


App Specification:

https://github.com/kbaseapps/kb_megahit/tree/dfbd3ad0467892b2b998796a02d4259fe7cc742f/ui/narrative/methods/run_megahit

Module Commit: dfbd3ad0467892b2b998796a02d4259fe7cc742f