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readme.txt 2019-11-07 1.2 kB
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MetaAnnotator-1.3.tar.gz 2018-10-21 11.3 MB
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MetaAnnotator User Guide Version 1.0

Install
1. download and extract MetaAnnotator.zip from
2. cd MetaAnnotator/
3. make
4. cd MetaCluster5.1 (MetaAnnotator uses a customized version of MetaCluster5)
5. make
6. cd ..  

Taxonomy tree preparation

prepare gid to tax id map file
1. download and extract dmp file from ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz
2. put gi_taxid_nucl.dmp in directory MetaAnnotator/tax

prepare node file
1. download and extract nodes.dmp from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdmp.zip
2. put nodes in directory MetaAnnotator/tax

Coding region preparation
1. download and extract coding_region.txt from the sourceforge repository
2. put coding_region.txt in directory MetaAnnotator/region


Usage

cd bin

Prepocessing database (once for each set of reference genomes) 
./buildindex.sh reference_folder_path dbname

Query

1. cluster the reads, output will be read.fa.cluster
./cluster.sh read.fa contig.fa dbname
(MetaAnnotator takes assembled contigs from query reads as input, and we recommend IDBA-UD as the assembler) 

2. Annotate each cluster with taxonomy, output will read.fa.annotation
./taxassign.sh read.fa dbname
Source: readme.txt, updated 2019-11-07