.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.7. .TH RUN_MAPSEMBLER2_PIPELINE "1" "October 2018" "run_mapsembler2_pipeline 2.2.4" "User Commands" .SH NAME run_mapsembler2_pipeline \- pipelines the mapsembler2 tools .SH SYNOPSIS .B run_mapsembler_and_phaser.sh \fI\,-s -r -t \/\fR[\fI\,1/2/3/4\/\fR]\fI\,\/\fR .SH DESCRIPTION run_mapsembler_pipeline.sh, a pipelining mapsembler2_extremities, mapsembler2_extend and kissread_g .SH OPTIONS .HP \fB\-s\fR: file containing starters (fasta) .HP \fB\-r\fR list of reads separated by space, surrounded by the '"' character. Note that reads may be in fasta or fastq format, gzipped or not. Example: \fB\-r\fR "data_sample/reads_sequence1.fasta data_sample/reads_sequence2.fasta.gz". .HP \fB\-t\fR: kind of assembly: 1=unitig (fasta), 2=contig (fasta), 3=unitig (graph), 4=contig(graph) .SS OPTIONAL .HP \fB\-p\fR prefix. All out files will start with this prefix. Example: \fB\-p\fR my_prefix .HP \fB\-k\fR value. Set the length of used kmers. Must fit the compiled value. Default=31. Example \fB\-k\fR 31 .HP \fB\-c\fR value. Set the minimal coverage. Default=5. Example \fB\-c\fR 5 .HP \fB\-d\fR value. Set the number of authorized substitutions used while mapping reads on found SNPs. Default=1. Example: \fB\-d\fR 1 .HP \fB\-g\fR value. Estimated genome size. Used only to control memory usage. e.g. 3 billion (3000000000) uses 4Gb of RAM. Default=10 million. Example: \fB\-d\fR 10000000 .HP \fB\-f\fR value. Set the process of search in the graph (1=Breadth and 2=Depth). Default=1. Example: \fB\-f\fR 1 .HP \fB\-x\fR value. Set the maximal nodes length . Default=40. Example: \fB\-x\fR 40 .HP \fB\-y\fR value. Set the maximal graph depth . Default=10000. Example: \fB\-y\fR 10000 .HP \fB\-h\fR Prints this message and exist .SH SEE ALSO Any further question: read the readme file or contact us: pierre.peterlongo@inria.fr .SH AUTHOR This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.