StrainPro -- a highly accurate Metagenomic strain-level profiling tool

Developers: Dr. Hsin-Nan Lin, Dr. Yaw-Ling Lin and Dr. Wen-Lian Hsu Institute of Information Science, Academia Sinica, Taiwan.

Introduction

Characterizing the taxonomic diversity of a microbial community is very important to understand the roles of microorganisms. Next generation sequencing (NGS) provides great potential for investigation of a microbial community and leads to Metagenomic studies. NGS generates DNA sequences directly from microorganism samples, and it requires analysis tools to identify microbial species (or taxonomic composition) and estimate their relative abundance in the studied community. Here we developed a novel metagenomic analysis tool, called StrainPro, which is highly accurate both at characterizing microorganisms at strain-level and estimating their relative abundances. A unique feature of StrainPro is it identifies representative sequence segments from reference genomes. We generate three simulated datasets using known strain sequences and another three simulated datasets using unknown strain sequences.

Download

Please use the command

  $ git clone https://github.com/hsinnan75/StrainPro.git

to download the package of StrainPro.

Dependencies

To compile StrainPro, it requires libboost-all-dev, libbz2-dev, and liblzma-dev installed in your system.

Compiling

Please change to StrainPro's folder and type 'make' to compile all programs of StrainPro.

Environment setting

setenv StrainPro_DIR StrainPro_download_path/bin

Testing

Please run "run_test.sh" to test StrainPro.

Taxonomy & Reference genomes

To download taxonomy information, please use the script "download_taxonomy.sh" to download taxonomy files (requisite for StrainPro).

  $./download_taxonomy.sh

If you have downloaded or customized taxonomy dump files, you may specify the file path and run StrainPro with '-dump TaxonomyPath'. StrainPro will find "nodes.dmp" and "merged.dmp" in the designated directory.

To download reference genomes, please use the script "download_genomic_library.sh" to download reference genomes.

  $./download_genomic_library.sh library (library: archaea | bacteria | viral | fungi | human)

The script will download all complete chromosomes/genomes of the designated library.

If you would like to use a customized reference library, please make sure your reference genomes follow the below requirements:

• Genome sequences are in FASTA format.
• Each sequence's header must contain the pattern of "taxid|xxxxx|" where xxxxx is the taxon ID. For example,

  taxid|562|NZ_CP027599.1 Escherichia coli strain 97-3250 ATCCCGGCCCCGGCAGAACCGACCTATCGTTCTAACGTAAACGT....

Database

To build a database, please use the StrainPro-build command

  $bin/StrainPro-build -r reference-fna -o ref_idx [ref_idx is the output folder for BWT indexes].

It will take a while to process the genome sequences and build BWT indexes.

Mapping & Profiling

To characterize the taxonomic composition of the input metagenomic data, please use the StrainPro-map command

  $bin/StrainPro-map -i idx -f read -o profile.txt [idx=BWT_index prefix / folder of BWT_indexes, read=NGS_dataset]

You may specify a specific index or a folder of multiple indexes. A specific index is designated with its prefix. The input NGS data is in FASTQ or FASTA format. Multiple files are separated with a space character. The output is a text file.

Output format

StrainPro ouputs the taxonomic composition of the input metagenomic data directly. The output format is

TaxID  Read_count  Est_depth   Est_relative_abundance   Confidence_score

where TaxID is the NCBI taxon identifier; Read_count is the number of reads that are classified into that taxon id; Est_depth is the estimated read depth of that taxon id; Est_relative_abundance is the estimated relative abundance (percentage); Confidence_score is the confidence score of that prediction.