NAME

       fsa_assemble - Constructs contigs from filtered overlaps and corrected reads

SYNOPSIS

       fsa_assemble [options] filterd_overlaps

DESCRIPTION

       Constructs contigs from filtered overlaps and corrected reads.

OPTIONS

       --min_length=INT

              minimum length of reads default: 0

       --min_identity=DOUBLE

              minimum identity of overlaps default: 0

       --min_aligned_length=INT

              minimum aligned length of overlaps default: 0

       --min_contig_length=INT

              minimum length of contigs default: 500

       --read_file=STRING

              read filename default: ""

       --overlap_file_type="|m4|m4a|paf|ovl"

              overlap  file  format.  "" = filename extension, "m4" = M4 format, "paf" = PAF format generated by
              minimap2, "ovl" = OVL format generated by FALCON.  default: ""

       --output_directory=STRING

              directory for output files default: "."

       --select_branch="no|best"

              selecting method when encountering branches in the graph, "no" = do not select any branch,  "best"
              = select the most probable branch default: "no"

       --thread_size=INT

              number of threads default: 1

       --dump=INT

              for testing, dump intermediate files default: 0

       --run_mode=INT

              for testing default: 4

       --lfc

              deprecated, for testing

       --remove_chimer

              deprecated, remove chimer node

       Usage: fsa_assemble [options] filterd_overlaps

              filterd_overlaps

              input filename

       --min_length=INT

              minimum length of reads default: 0

       --min_identity=DOUBLE

              minimum identity of overlaps default: 0

       --min_aligned_length=INT

              minimum aligned length of overlaps default: 0

       --min_contig_length=INT

              minimum length of contigs default: 500

       --read_file=STRING

              read filename default: ""

       --overlap_file_type="|m4|m4a|paf|ovl"

              overlap  file  format.  "" = filename extension, "m4" = M4 format, "paf" = PAF format generated by
              minimap2, "ovl" = OVL format generated by FALCON.  default: ""

       --output_directory=STRING

              directory for output files default: "."

       --select_branch="no|best"

              selecting method when encountering branches in the graph, "no" = do not select any branch,  "best"
              = select the most probable branch default: "no"

       --thread_size=INT

              number of threads default: 1

       --dump=INT

              for testing, dump intermediate files default: 0

       --run_mode=INT

              for testing default: 4

       --lfc

              deprecated, for testing

       --remove_chimer

              deprecated, remove chimer node

Constructs contigs from filtered overlaps and co... July 2020                                    FSA_ASSEMBLE(1)