MaGuS

MaGuS (Map-GUided Scaffolding) is a scaffolder and a reference-free evaluator of assembly quality. It uses a draft genome assembly, a genome map, and high-throughput sequencing paired-end data. It has been succesfully tested on the Arabidopsis genome with Illumina reads and a Whole-Genome Profiling (WGP) map.

MaGuS run the five following steps :

- wgp2map: create a map genome file based on WGP data.
- map2qc: analyse the assembly quality based on colinearity between the assembly and the map.
- map2links: create links (map-links) between scaffolds .
- pairs2links: use NGS data to validate the map-links, orient the scaffolds and estimate the gaps size and create a '.de'.
- links2scaf: output the new final assembly in fasta format.

The use of MaGuS is not restricted to WGP data, other map types can be used. However they have to be formatted in the MaGuS map format (see below).

GroupID 1
Tag1 Tag2 Tag3 Tag4 Tag4 Tag5 Tag6 Tag7
rank1 rank2 rank3 rank4 rank5 rank6 rank7 
GroupID 2
...

MaGuS is distributed open-source under CeCILL FREE SOFTWARE LICENSE. Check out http://www.cecill.info/ for more information about the contents of this license.

MaGuS website http://www.genoscope.cns.fr/magus

Contact : magus [a] genoscope [.] cns [.] fr

PRE-REQUIREMENTS

• A Linux based operating system.
• Perl 5.10.1 or higher installed.
• Perl GetOpt::Long module (http://search.cpan.org/dist/Getopt-Long/)
• Perl FileHandle module (http://search.cpan.org/dist/FileHandle/)
• Perl Moose module (http://search.cpan.org/dist/Moose/)
• Perl Switch module (http://search.cpan.org/dist/Switch/)
• samtools 0.1.19
• SGA 0.10.13
• R 3.0.2 (cran.r-project.org)

DEPENDENCIES

INSTALLATION

1. Download the .zip file MaGuS-master:
   wget https://github.com/institut-de-genomique/MaGuS/archive/master.zip
2. Unzip it:
   unzip master.zip
3. Download the example dataset available on the website http://www.genoscope.cns.fr/magus or:
   wget http://www.genoscope.cns.fr/magus/datasets/MaGuS/Arabido/Arabido_data.tar.gz
4. Untar/unzip it:
   tar -zxvf Arabido_data.tar.gz
5. Add MaGuS libraries in $PERL5LIB (i.e. PERL5LIB=$(pwd)/MaGuS-master/magus-1.0/lib/:$PERL5LIB)
6. Add MaGuS binaries in $PATH (i.e. PATH=$(pwd)/MaGuS-master/magus-1.0/bin/:$PATH)
7. Run MaGuS on the example data set and specify paths to SGA, R and samtools if they are not in the path :

$ magus all -w Arabido_data/tagsWgp.out -t Arabido_data/mapped_tag.bam -b Arabido_data/mp_map1_2.bam,5414,1000,76 -b Arabido_data/mp_map2_2.bam,5414,1000,76 -f Arabido_data/Arabido.fa -p Arabido -e 119667750 -sga /path/to/SGA/ -r /path/to/R/ -samtools /path/to/samtools/

RUNNING MaGuS

There are two ways to run MaGuS. The most common way is:

 magus all -w wgpFile -t tags.bam -f assembly.fa -e estimate_size -b file.bam,m,sd,s

The second way is to run MaGuS pipeline step by step as:

• step1:

magus wg2map -w wgpFile -t tags.bam

• step2:

magus map2qc -f assembly.fa -e estimate_size -s tags_coordinates.txt

• step3:

magus map2links -a anchoring_file.txt

• step4:

magus pairs2links -f assembly.fa -l links_file.txt -b file.bam,m,sd,s

• step5:

magus links2scaf -f assembly.fa -c links.de

OPTIONS

• Options for all (wgp2map-map2qc-map2links-pairs2links-links2scaf)

     -w <string>    wgpFile: WGP data
     -t <string>    tags.bam: tags alignment on the assembly (BAM)
     -f <string>    assembly.fa: assembly file (FASTA)
     -e <int>       estimate_size: genome estimate size (bp)
     -b <string>    file.bam,m,sd,s: paired reads alignment (BAM), library median size (bp), library standart deviation (bp), reads size (bp)
  
     OPTIONAL PARAMETERS:
     -s <string>    sorted file according to mapping position of tags       (default : prefix_tags_coordinates.txt)
     -a <string>    anchored tags on assembly       (default : prefix_anchored_assembly.txt)
     -l <string>    output file containing links between contigs/scaffolds  (default : prefix_map_links.txt)
     -c <string>    file containing links in DE format      (default : prefix_validated_map_links.de)
     -samtools <string>    path to samtools        (default: $PATH)
     -r <string>    path to R       (default: $PATH)
     -sga <string>    path to sga     (default: $PATH)
     -p <string>    prefix for output files (default: magus)
     --no-plot      disable plot output
     -h             this help
  

• Options for wgp2map

    -w <string>     wgpFile: WGP data
    -t <string>     tags.bam: tags alignment on the assembly (BAM)
  
    OPTIONAL PARAMETERS:
    -p <string>     prefix for output files (default : magus)
    -samtools <string>     path to samtools        (default: $PATH)
    -h              this help
  

• Options for map2qc

    -f <string>     assembly.fa: assembly file (FASTA)
    -e <int>        estimate_size: genome estimate size (bp)
    -s <string>     tags_coordinates.txt: sorted file according to mapping position of tags
  
    OPTIONAL PARAMETERS:
    -p <string>     prefix for output files (default: magus)
    -r <string>     path to R       (default: $PATH)
    --no-plot       disable plot output
    -h              this help
  

• Options for map2links

    -a <string>     anchoring_file.txt: anchored assembly (wgp2map output)
  
    OPTIONAL PARAMETERS:
    -l <string>     output file containing links between contigs/scaffolds  (default: prefix_map_links.txt)
    -p <string>     prefix for output files (default: magus)
    -h              this help
  

• Options for pairs2links

    -f <string>     assembly.fa: assembly file (FASTA)
    -l <string>     links_file.txt: file containing links between contigs/scaffolds
    -b <string>     file.bam,m,sd,s: paired reads alignment (BAM), library median size (bp), library standart deviation (bp), reads size (bp)
  
    OPTIONAL PARAMETERS:
    -samtools <string>     path to samtools        (default: $PATH)
    -p <string>     prefix for output files (default: magus)
    -h              this help
  

Several mapped paired-end libraries (BAM file) can be used simultanously with the -b option for each one of them. Example:

magus pairs2links -f Arabidopsis.fa -l links_file.txt -b mapping_library1.bam,3500,600,101 -b mapping_library2.bam,6000,1000,151 -samtools /path/to/samtools/ -p Arabido

• Options for links2scaf

    -f <string>     assembly.fa: assembly file (FASTA)
    -c <string>     links.de: file containing links in DE format
  
    OPTIONAL PARAMETERS:
    -sga <string>     path to sga     (default: $PATH)
    -p <string>     prefix for output files (default: magus)
    -h              this help
  

OUTPUT

• wgp2map output

-${prefix}_tags_coordinate.txt: File containing anchored tags on assembly sorted by mapping position

col 1: scaffold ID
col 2: position
col 3: tagId
col 4: rank col 5: group ID

-${prefix}_anchored_assembly.txt: MaGuS format File of anchored scaffolds on the genome map

col 1: group ID
col 2: scaffold ID col 3: minimum tag rank col 4: maximum tag rank col 5: number of tags

• map2qc output -prefix_An.csv: Anx values for x = 1 to 100%
  -prefix_AnA.csv: AnAx values for x = 1 to 100%
  -prefix_AnG.csv: AnGx vlaues for x = 1 to 100%
  -prefix_quality_metrics.png: Anx, AnAx and AnGx plots
  -prefix_quality_metrics.txt: summary quality metrics of Anx, AnAx and AnGx values for x=0.5, x=0.75 and x=0.9

• map2links output -${prefix}_map_links.txt: list of map-links between scaffolds (scaf1_scaf2)

• pairs2links output -${prefix}_validated_map_links.de: map-links validated by paired reads in .de format (SGA specific format)
  -${prefix}_unvalidated_map_links.txt: list of map-links not validated by the paired reads -${prefix}_besst_validated_map_links.log: links statistics
  -output_coord_links: repository containing one file by linkage between two scaffold according to the orientation. The format name of these files is scafID1_scafID2_orientationRead1orientationRead2 (ex: scaffold88_scaffold459_+-). Each line of these file contains linkage information generated by one read. The output format is:

col 1: scafID1
col 2: scafID2
col 3: scafID1 length col 4: scafID2 length col 5: scafID1 orientation
col 6: scafID2 orientation
col 7: scafID1 mapping position col 8: scafID2 mapping position col 9: gap size

• links2scaf output -${prefix}_final_scaffolds.fa: the final assembly (FASTA) -${prefix}_scaffolds.fa: SGA scaffolding output (FASTA) -${prefix}_unused_scaffolds.fa: scaffold not used for scaffolding step (FASTA)
  -${prefix}_sga_scaf_unused.txt: list of scaffolds not considered by SGA -${prefix}_sga.scaf: scaffolding information (SGA specific format)
  -${prefix}_sga_scaffold2fasta.log: scaffolding statistics (SGA specific format) -${prefix}_sga_scaffold.log: scaffolding statistics/informations (SGA specific format)

More informations

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If you have questions about MaGuS, you may ask them to amadoui [at] genoscope [.] cns [.] fr, cdossat [at] genoscope [.] cns [.] fr, ldagata [at] genoscope [.] cns [.] fr and jmaury [at] genoscope [.] cns [.] fr . You may also create an issue to ask questions on github website: https://github.com/institut-de-genomique/MaGuS/issues.

ACKNOWLEDGMENTS

Carole Dossat, d'Agata Léo, Jean-Marc Aury and Mohammed-Amin Madoui - MaGuS's authors

This work was financially supported by the Genoscope, Institut de Genomique, CEA and Agence Nationale de la Recherche (ANR), and France Génomique (ANR-10-INBS-09-08).