Quick Start

git clone https://github.com/derekguan/deSPI.git

cd deSPI/src

make

cd ..

./deSPI-download -o taxonomy taxonomy  

./deSPI-index test/refs/ref2tid.map taxonomy/nodes.dmp bin index

bin/deSPI classify index test/reads/reads.fa >Labels

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Introduction

deSPI is a novel metagenomics reads classification tool which classifies reads by recognizing and analyzing short exact matches between reads and references with de Bruijin graph-based lightweight reference indexing.

deSPI is mainly designed by Dr. Bo Liu and developed by Mr. Dengfeng Guan with the supervision of Prof. Yadong Wang in Center for Bioinformatics, Harbin Institute of Technology, China.

Parameters

deSPI-download

deSPI-download [<options>] <database>

ARGUMENT
 <database>        One of refseq, genbank, or taxonomy:
                     - use refseq or genbank for genomic sequences,
                     - taxonomy for taxonomy mappings.

COMMON OPTIONS
 -o <directory>         Directory to which the files are downloaded. Default: '.'.
 -P <# of threads>      Number of processes when downloading (uses xargs). Default: '1'

WHEN USING database refseq OR genbank:
 -d <domain>            What domain to download. One or more of bacteria, viral, archaea (comma separated).
 -a <assembly level>    Only download genomes with the specified assembly level. Default: 'Complete Genome'.
 -c <refseq category>   Only download genomes in the specified refseq category. Default: any.
 -g                     Download GI map.

deSPI-index

deSPI-index <TID_REF_MAP> <NODE_PATH> <DESPI_BIN_DIR> <INDEX_DIR>

ARGUMENT
    <TID_REF_MAP>            map file list reference path and its taxonomy id.
    <NODE_PATH>              location of nodes.dmp file.
    <DESPI_BIN_DIR>          directory of deSPI execuative files.
    <INDEX_DIR>              directory to store deSPI's index.

deSPI classify

Usage:     deSPI  classify  [Options] <IndexDir> <ReadFiles>

<IndexDir>              the directory of index
<ReadFiles>             reads files, in FASTQ/FASTA format (separated by space)

Options:   -s, --seed_len      <uint8_t>          lower bound of seed length from 24 [24]
           -t, --threads       <int>              number of threads [1]
           -i, --seed_step     <int8_t>           seed step size [4]
           -p, --paired        <int8_t>           set for paired end reads [False]
           -h, --help                             help

deSPI view

Usage:     deSPI  view  [Options] <IndexDir> 

<IndexDir>              the directory of index

Options:   -x, --taxid      <uint32_t>+          extract unitigs corresponding to the taxonomy id, use 
                                                 comma to join mulitple taxids. If not given output 
                                                 all unitigs 
           -h, --help                            help

Memory Requirements

The memory footprint of deSPI is relatively small for read classification, e.g., using the 12274 RefSeq complete genomes (5975 bacterial, 219 archaea, 6080 viral genomes) as reference, deSPI requires 25 gigabytes to classify the input reads. However, it is worthnoting that, deSPI requires relatively large memory to construct the reference index, e.g., it requires over 100 gigabytes to construct the index of RefSeq complete genomes. This is mainly due to the index construction of deSPI is still under optimization.The memory footprint will be much lower in the later version.

User's Guide

Database download

Users can take the following command to build their own reference library. All reference genomes will be download from NCBI genbank or refseq.

cd deSPI

bin/deSPI-download -o LOCAL_REF_DIR -P THREAD_NUM -d DOMAIN DATABASE 

DOMAIN includes viral, bacteria, archaea

DATABSE includes refseq, genbank, taxonomy

Index construction

After creating a reference library, the reference index can be constructed by the following command. Since deSPI needs nodes.dmp as input, nodes.dmp requires be downloaded in advance (recommend to use deSPI-download).

cd deSPI

bin/deSPI-index  $LOCAL_REF_DIR/ref2tid.map taxonomy/nodes.dmp bin INDEX_DIR

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Read classfication

With the constructed index, use the following command to run deSPI to classify reads.

cd deSPI

bin/deSPI classify INDEX_DIR READS_FILES >Labels

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Output Format

Each sequence classified by deSPI outputs a single line. Each line contains four/three tab-delimited fields; from left to right, they are:

1. "C"/"U": the letter indicates whether the sequence is classified or not.
2. The sequence ID, obtained from the FASTA/FASTQ header.
3. The taxonomy ID used to label the sequence; 0 if the sequence is unclassified.
4. the score of Labels, could be missing if there is no match between read and references.

For example:

       C	ERR636248.35	177416	177416:191           

indicates that the Sequence "ERR636248.35" is assigned to taxononmy ID 177416, and the score of 177416 is 191.

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Real sequencing and Simulated datasets

We benchmarked deSPI with mainly three experiments, including a simulated dataset test (20 million reads in total), 559 real sequencing datasets test and a real metagenomics dataset test from human gut.

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Contact

For advising, bug reporting and requiring help, please contact [email protected]