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Tools Overview

Tool	Paper	Code	Tutorial	Our Results	Team Members
Kraken	kraken-paper	kraken-code	kraken-tutorial	preliminary-results	Dongjo
CLARK	clark-paper	clark-code	clark-tutorial	CLARK-results	Tomas
SURPI	surpi-paper	surpi-code	surpi-turial	-	Vishnu
MetaPhlAn2	MetaPhlAn-paper	MetaPhlAn-code	MetaPhlAn-turial	Tool Evaluation	Juichang Lu
PaPrBaG	PaPrBaG-paper	PaPrBaG-code		-	Vasanta
Phylosift	Phylosift-paper	Phylosift-code	Phylosift-tutorial	-	Yihao Ou
MetaSPAdes	MetaSPAdes-paper	MetaSPAdes-code	-	MetaSPAdes-results	Vishnu
bowtie2	bowtie2-paper	bowtie2-code	bowtie2-tutorial	bowtie-results	Vasanta
MGmapper	MGmapper paper	MGmapper code	MGmapper tutorial	Preliminary evaluation	Juichang Lu

Retrieving NCBI taxonomy IDs

Setup

1. Download pre-formatted DB for nt (nt.*tar.gz) from NCBI.

2. Download BLAST taxonomy DB from NCBI.

3. Extract all tar.gz to a directory.

4. Set environment variable indicating location of BLAST DB to be used in the BLAST run.

   export BLASTDB=[path-to-dir]

BLAST

1. The input for blastn, all.fasta, was created by using cat on all of the reference genome for the challenge.

2. The taxonomy IDs were retrieved by running the following command:

   blastn -db nt -query all.fasta -max_target_seqs 1 -max_hsps 1 -outfmt "6 qseqid staxid ssciname scomname pident evalue" -out refGenomeTaxMapping.tsv

Refer to this link for details on supported output formats for blastn.