Finishing bacterial genome assemblies with Mix
Mix is a tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a path in the extension graph that maximizes the cumulative contig length.
Datasets corresponding to the benchmarks analyzed in the manuscript as well as supplemenatary figures are available at the accompanying website
Mix was implemented in Python and tested under Linux environment. It has the following requirements :
- python 2.7 (http://www.python.org/)
- python-networkx 1.6-2 (http://networkx.lanl.gov/)
- Biopython (http://biopython.org/wiki/Main_Page)
- MUMmer 3.22 (http://mummer.sourceforge.net/).
Mix can be downloaded at :
You can get the latest version of the development via this github link.
To install the software, the user must download the file Mix-master.zip (see previous section) and extract it
tar -xzf Mix-master.zip
Mix runs in a command line environment. The package contains one main script called Mix.py that coordinates the execution of the whole process. This section describes how the user must call it.
Mix takes an alignment file and a file containing all the contigs (in fasta format) as input. The alignment file must be in coords format, obtained with MUMmer and the following command lines :
nucmer -prefix=alignments contigs.fa contigs.fa
show-coords -rcl alignments.delta > alignments.coords
The file "contigs.fa" contains the contigs of all the assemblies that have to be mixed (two or more). This file which concatenate all the assemblies is generated by running the script called "preprocessing.py".
Usage: Mix.py [options]
Options:
-h, --help show this help message and exit
-a ALN, --aln=ALN the file containing the alignments (.coords)
-o OUT, --out=OUT the output directory where the scaffolds will be
written (it must already exist)
-c CTG, --ctg=CTG the multi FASTA file containing all the contigs that
were used in the alignment
-A ATH, --ath=ATH minimum length of alignment (default:0)
-C CTH, --cth=CTH minimum length of contig (default:500)
-d, --dot write the graphs in dot format
-g, --graph write the graphs in cytoscape format
-r, --restrict-to-aligned
If on, restrict output to aligned coords
For the current version applied on bacterial assemblies, recommanded parameters values are -A 500 -C 0.
The output assembly will be in the file:
<specified_output_dir>/Mix_results_A<aln_threshold>_C<contig_threshold>/scaffolds.fa
along with statistics and graphs about the final assembly in the files
<specified_output_dir>/Mix_results_A<aln_threshold>_C<contig_threshold>/initial_assembly_graph.gml
<specified_output_dir>/Mix_results_A<aln_threshold>_C<contig_threshold>/reduced_assembly_graph.gml
<specified_output_dir>/Mix_results_A<aln_threshold>_C<contig_threshold>/all_alignments.csv
<specified_output_dir>/Mix_results_A<aln_threshold>_C<contig_threshold>/all_contigs.csv
The two assembly graphs can also be saved in the cytoscape or dot format by setting the corresponding command line flags.
<your_path_to_Mix>/Mix-<version>/bin/preprocessing.py -o contigs.fa Assembly1.fa Assembly2.fa [Assembly3.fa]
nucmer --maxmatch -c 30 -l 30 -banded -prefix=alignments contigs.fa contigs.fa
show-coords -rcl alignments.delta > alignments.coords
<your_path_to_Mix>/Mix-<version>/bin/Mix.py -a alignments.coords -c contigs.fa -o output_dir/ -C 300 -A 200
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This requires QUAST (>= 2.1) in addition to MIX requirements. QUAST can be downloaded on the SF website.
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The provided Makefiles rules to regenerate results presented in the RECOMB-CG paper expect QUAST to be installed in bin/quast2-1. Please update the headers in all Makefile to point to any other QUAST installation.
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The script expect MUMmer in bin/MUMmer. We recommend to create a symlink from quast-2.1/libs/MUMmer3.23-ARC to bin/MUMmer
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Datasets for Mycoplasmas studies are available on the accompanying website. We provide a script batch download tool in ``datasets/Mycoplasmas/get_mycoplasmas.sh'' .
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Once QUAST, MUMmer and the datasets have been obtained, one can generate all the quasts reports for the 10 mycoplasmas by running ``make ALLMYCOQUASTS'' in the root Mix folder. This will take some time (~10 min on MacBook Pro i5) and will generate and populate the following files and folders :
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temp_assemblies/*.fasta: Concatenated fasta files of the input assemblies
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temp_assemblies/*.coords *.delta: MUMmer results for self-alignement of FASTA files
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temp_assemblies/*.mix.log.txt: Log of Mix execution
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result_assemblies/*_mix.fasta: Resulting merged after execution of Mix
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result_statistics/all_myco/*_QUAST: QUAST report for each species, where the 19 resulting assemblies (for single-assemblies, GAA, GAM-NGS and mix) are compared
Copyright (c) 2013 Hayssam Soueidan (1) (massyah@gmail.com)
Florence Maurier (2) (florence.maurier@u-bordeaux2.fr)
Alexis Groppi (2) (alexis.groppi@u-bordeaux2.fr)
Macha Nikolski (3) (macha@labri.fr)
(1) NKI-AVL, Plesmanlaan 121,
1066 CX Amsterdam, Netherlands
(2) CBiB - Universite Victor Segalen Bordeaux,
146, rue Leo Saignat, 33076 Bordeaux, France
(3) CNRS / LaBRI, Universite Bordeaux 1, 351 cours de la Liberation,
33405 Talence Cedex, France
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The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
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