man run_mapsembler2_pipeline (1): manual page for run_mapsembler2

SYNOPSIS

run_mapsembler_and_phaser.sh ,-s <starter.fasta> -r <reads.faste> -t /[,1/2/3/4/],<options>/

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)

: -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

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