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
wget https://github.com/institut-de-genomique/MaGuS/archive/master.zipunzip master.zipwget http://www.genoscope.cns.fr/magus/datasets/MaGuS/Arabido/Arabido_data.tar.gztar -zxvf Arabido_data.tar.gzPERL5LIB=$(pwd)/MaGuS-master/magus-1.0/lib/:$PERL5LIB)PATH=$(pwd)/MaGuS-master/magus-1.0/bin/:$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/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,sThe second way is to run MaGuS pipeline step by step as:
magus wg2map -w wgpFile -t tags.bammagus map2qc -f assembly.fa -e estimate_size -s tags_coordinates.txtmagus map2links -a anchoring_file.txtmagus pairs2links -f assembly.fa -l links_file.txt -b file.bam,m,sd,smagus links2scaf -f assembly.fa -c links.de -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-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-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-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-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 helpSeveral 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-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: $PATH)
-p <string> prefix for output files (default: magus)
-h this help-${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: scaffold88scaffold459+-). 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
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.
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).