Metagenomic Binning through Multi-resolution Genomic Binary Patterns
C++ Makefile
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LICENSE
README.md
dbscan.cpp
dbscan.h
factorisation.h
feature_extraction.h
help.h
kmeanspp.h
load.h
main.cpp
main.o
makefile
nucreps.h
oned_lbp.h
sptree.cpp
sptree.h
tsne.cpp
tsne.h
vptree.h

README.md

program name: MrGBP version: 1.0 Developer: Samaneh Kouchaki (kouchaki.samaneh@gmail.com)

========dependencies Install the following dependencies

eigen3: http://eigen.tuxfamily.org/index.php?title=Main_Page boost: http://www.boost.org/doc/libs/1_62_0/more/getting_started/unix-variants.html methgl: http://mathgl.sourceforge.net/doc_en/Installation.html

for suggest using g++-4.8 or g++-4.9

if you are installing dependencies locally please add the path to the makefile ========instalation guide

(1) run: make code is ready to use

========whtat does the code do: It is for binning metagenomic contigs.

========support platform MrGBP has been tested on both Mac and Linux platforms.

========run There is a number of options:

-fa : the fasta file to be processed by MLBP_BIN

-svdd : the SVD dimension, default: 60

-mlbpn : the MLBP window length, default: 8

-outdir : a directory that all the MLBP_BIN results will be saved including cluster labels and .png figure

-no_clust : the number of clusters for kmeans++, default: 10

-covpm : a file contains average coverage depth; the entries should be seprated by single space

-covpstd : a file contains standard deviation coverage depth; the entries should be seprated by single space

-reps : the numerical mapping including EIIP, Real, Integer, Paired, Atomic, default: Integer

-clust : the clustering method kmeans++ or dbscan: dbscan

-dbep : the epsilon for dbscan, default: 0.02

-dbminpt : the number of minimum neighbouring points for dbscan, default: 8

-save_feat : If the features needs to be saved separately.

-no_dims : bh-tSNE dimensions, defualt: 2.

examples:

  1. Running with default option on a fasta file indicated by the path and save the results in desired directory

./MrGBP -fa /pathtofile/file.fa -outdir /pathtofile/file.fa

  1. Check the available options

./MrGBP -help

  1. run using coverage profile

./MrGBP -fa /pathtofile/file.fa -covpm /pathtofile/cpm -covpstd /pathtofile/cpstd

Codes for kmeans++ and dbsacan have been downloaded and modified to match our code: kmeans++: http://rosettacode.org/wiki/K-means%2B%2B_clustering dbscan: https://github.com/propanoid/DBSCAN

if there is any question or any bug please email me at kouchaki.samaneh@gmail.com