bionic (1) run_mapsembler2_pipeline.1.gz
NAME
run_mapsembler2_pipeline - manual page for run_mapsembler2_pipeline 2.2.4+dfsg
SYNOPSIS
run_mapsembler_and_phaser.sh -s <starter.fasta> -r <reads.faste> -t [1/2/3/4]<options>
DESCRIPTION
run_mapsembler_pipeline.sh, a pipelining mapsembler2_extremities, mapsembler2_extend and kissread_g
-s: file containing starters (fasta) -r list of reads separated by space, surrounded by the '"'
character. Note that reads may be in fasta or fastq format, gzipped or not. Example: -r
"data_sample/reads_sequence1.fasta data_sample/reads_sequence2.fasta.gz". -t: kind of assembly:
1=unitig (fasta), 2=contig (fasta), 3=unitig (graph), 4=contig(graph)
<options>:
-p prefix. All out files will start with this prefix. Example: -p my_prefix -k value. Set the
length of used kmers. Must fit the compiled value. Default=31. Example -k 31 -c value. Set the
minimal coverage. Default=5. Example -c 5 -d value. Set the number of authorized substitutions
used while mapping reads on found SNPs. Default=1. Example: -d 1 -g value. Estimated genome size.
Used only to control memory usage. e.g. 3 billion (3000000000) uses 4Gb of RAM. Default=10
million. Example: -d 10000000 -f value. Set the process of search in the graph (1=Breadth and
2=Depth). Default=1. Example: -f 1 -x value. Set the maximal nodes length . Default=40. Example:
-x 40 -y value. Set the maximal graph depth . Default=10000. Example: -y 10000 -h Prints this
message and exist
Any further question: read the readme file or contact us: pierre.peterlongo@inria.fr
SEE ALSO
The full documentation for run_mapsembler2_pipeline is maintained as a Texinfo manual. If the info and
run_mapsembler2_pipeline programs are properly installed at your site, the command
info run_mapsembler2_pipeline
should give you access to the complete manual.