Megahit

Next Friday, June 24, we’ll discuss this paper:

Li et al: MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. 2015 Bioinformatics.

Megahit is an assembler for metagenomics data. It was developed to work on large, complex datasets.  It’s available from github, and doesn’t do any pre-processing for you.

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Kraken: taxonomic sequence classification system

We will discuss this paper on Friday, April 22nd from noon-1pm:

Wood DE, Salzberg SL: Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biology 2014, 15:R46.

Obtain software from here.

Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.

Have any installation/running questions? Ask here.