Man page - fsa_assemble(1)

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Package: mecat2
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mecat2

Manual

FSA_ASSEMBLE

NAME
SYNOPSIS
DESCRIPTION
OPTIONS

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