HuangYukun/megagta

HMM-guided metagenomic gene-targeted assembler using iterative de Bruijn graphs

MegaGTA

Getting Started

git clone https://github.com/HKU-BAL/megagta.git
cd megagta
git submodule update --init --recursive
./make.sh

# assemble with default parameters
bin/megagta.py -r reads.fq -g gene_list.txt -o output_dir

# post-processing with clustering similarity threshold 0.99 (i.e. 1-0.01)
bin/post_proc.sh -g gene_resources_dir -d output_dir/contigs -m 16G -c 0.01

Required Tools

• HMMER 3.1 (http://hmmer.janelia.org)
• UCHIME (http://drive5.com/usearch/manual/uchime_algo.html)
• ant 1.9.2 or greater (for compiling RDPTools)
• g++ 4.6 or greater (for compiling MegaGTA core)

Simple Settings

• In bin/post_proc.sh users are supposed to modidy the paths for HMMER & UCHIME to their own ones.

• gene_list.txt is a config file. Each line of the file specifying interested genes and some of their information required by the assembly, including forward/reverse HMM, and the reference multiple sequence alignment of that gene family. Following is an example.

rplB share/RDPTools/Xander_assembler/gene_resource/rplB/for_enone.hmm share/RDPTools/Xander_assembler/gene_resource/rplB/rev_enone.hmm share/RDPTools/Xander_assembler/gene_resource/rplB/ref_aligned.faa
nirK share/RDPTools/Xander_assembler/gene_resource/nirK/for_enone.hmm share/RDPTools/Xander_assembler/gene_resource/nirK/rev_enone.hmm share/RDPTools/Xander_assembler/gene_resource/nirK/ref_aligned.faa

• gene_resources_dir is an input folder for post-processing which follows the format Xander assembler used. It can be found through:

megagta/share/RDPTools/Xander_assembler/gene_resource

• If genes not included are in interest, please follow the README file of Xander to prepare the resource.