RAMBL: Large-scale 16S gene assembly using metagenomic shotgun sequences

Created by Feng Zeng Summer 2015.

Overview

RAMBL is a tool for the assembly of full-length 16S genes in metagenomic shotgun data. RAMBL devices a taxonomic tree search to partition data into subgroups that comprise of short reads yielded from similar strain sequences. Within each subgroup, RAMBL deploys a progressive Dirichlet Process mixture clustering method to reconstruct full-length 16S gene sequences.

Dependency

Following tools are all assumed installed and could be found in system environment:

* Python >= 2.7.10
* GCC >= 4.9.1
* Bowtie2 >= 2.2.4
* Samtools == 0.1.19
* Bedtools >= 2.24.0
* Sickle >= 1.33
* Seqtk >= 1.0

Following Python packages are all assumed installed:

* ETE2 Toolkit >= 2.3.1
* Scipy >= 0.15.1
* Numpy >= 1.9.2
* Scikit-bio == 0.4.0
* Biopython >= 1.65

Installation

Set up environment variable:
```
$ export CXX=<PATH TO G++4.9>
```

Clone the repository:

$ git clone https://github.com/homopolymer/RAMBL.git

Build and install to $PWD/bin:

$ python setup.py install --prefix=$PWD

16S Database

RAMBL relies on GreenGenes, which is available at ftp://greengenes.microbio.me/greengenes_release/gg_13_8_otus/. The rrnDB file that records gene copy number for GreenGenes is contained in the RAMBL package.

To download GreenGenes:

$ bash download_greengenes.sh

Usage

$ python rambl.py [-c cores] [-v] [-p output_prefix] data_info.txt

Data Metainfo

In the above, the argument 'data_info.txt' is a metadata file. It contains the following contents:

Sequencing data
1. BamFiles=<FILE>, a file listing the mapping files of data against 16S rRNA reference, one BAM file per line.
```
$ ls -A1 *_to_gg_99_otus.bam | xargs realpath > bams.fofn
```
Gene data
1. GeneSeq=<FILE>, a FASTA file storing the reference sequences of 16S rRNA genes.
2. GeneIndex=<FILE>, the FASTA index file.
3. GeneTree=<FILE>, a Newick file recording the phylgenetic tree of 16S rRNA genes.
4. GeneTax=<FILE>, a taxonomic annotation of 16S rRNA genes.
5. GeneAlign=<FILE>, a FASTA file of 16S sequence alignments.

Test

The repository RAMBL_Test contains data and script to test whether RAMBL installs and works correctly. Download test data and run the following codes for test:

$ cd test
$ python make_datainfo.py
$ python <PATH TO rambl.py> -c 20 -v data_info.txt 2>&1 | tee log.txt
$ less log.txt

Development Team

Feng Zeng, Xiamen University
Zicheng Wang, Tsinghua University
Ying Wang, Xiamen University
Ting Chen, Tsinghua University

homopolymer / RAMBL