NAME

       lamassemble - Merges overlapping "long" DNA reads into a consensus sequences

SYNOPSIS

       lamassemble [options] last-train.out sequences.fx > consensus.fa

DESCRIPTION

       Merge DNA sequences into a consensus sequence.

OPTIONS

       -h, --help
              show this help message and exit

       -a, --alignment
              print an alignment, not a consensus

       -c, --consensus
              just make a consensus, of already-aligned sequences

       -g G, --gap-max=G
              use alignment columns with <= G% gaps (default=50)

       --end  ... including gaps past the ends of the sequences

       -s S, --seq-min=S
              omit consensus flanks with < S sequences (default=1)

       -n NAME, --name=NAME
              name of the consensus sequence (default=lamassembled)

       -o BASE, --out=BASE
              just write MAFFT input files, named BASE.xxx

       -p P, --prob=P
              use pairwise restrictions with error probability <= P (default=0.002)

       -d D, --diagonal-max=D
              max change in alignment diagonal between pairwise alignments (default=1000)

       -v, --verbose
              show progress messages

       --all  use all of each sequence, not just aligning part

       --mafft=ARGS
              additional arguments for MAFFT

              LAST options:

       -P P   number of parallel threads (default=1)

       -W W   use minimum positions in length-W windows (default=19)

       -m M   max initial matches per query position (default=5)

       -z Z   max gap length (default=30)