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RUN_MAPSEMBLER2_PIPELINE

NAME

run_mapsembler2_pipeline − manual page for run_mapsembler2_pipeline 2.2.3+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 DOT peterlongo AT inria DOT 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.

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