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Epigenetic Metagenomic Motif Characterization Assembler

This tool uses epigenetically modified motifs to fine map the bacterial genomes present in mixed metagenomic samples. The output is fully assembled genomes present in the metagenomic sample.

##Running To run the code simply type:

sh EMMCAssemble.sh [reference.fasta] [nat.cmp.h5] [motif file] [best.edges] [name] [gkpStore] [tigStore]

reference.fasta: reference fasta file for the metagenomic sample

nat.cmp.h5: cmph5 file for the native (NOT WGA) metagenomic sample

motif file: a file listing the motifs and epigenetically modified positions. An example is included here as "example_motif.txt"

best.edges: the best.edges file produced by Celera Assembler from the unitigger

name: the name tag for the files created

gkpStore: path for the celera assembler gkpStore

tigStore: path for the celera assembler tigStore

• PYTHON
• pbtools
• pbcore
• numpy
• h5py
• shlex
• subprocess
• networkx
• matplotlib

To cite the code, please refer to:

##Questions Please contact elizabeth.webster@icahn.mssm.edu