---
name: "fsa_assemble"
section: "1"
platform: "linux"
package: "mecat2"
version: "0.0+git20200428.f54c542+ds-4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fsa_assemble"
---

# fsa\_assemble(1)

Constructs contigs from filtered overlaps and corrected reads

## 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