---
name: "fml-asm"
section: "1"
platform: "linux"
package: "fml-asm"
version: "0.1+git20221215.85f159e-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fml-asm"
---

# fml-asm(1)

assemble Illumina short reads in small regions

## NAME

fml-asm - assemble Illumina short reads in small regions

## SYNOPSIS

**fml-asm** \[*options*\] *\<in.fq\>*

## OPTIONS

- **-e** INT

  k-mer length for error correction (0 for auto; **-1** to disable) \[0\]

- **-c** INT1\[,INT2\]

  range of k-mer & read count thresholds for ec and graph cleaning \[4,8\]

- **-l** INT

  min overlap length during initial assembly \[33\]

- **-r** FLOAT

  drop an overlap if its length is below maxOvlpLen\*FLOAT \[0.7\]

- **-t** INT

  number of threads (don't use multi-threading for small data sets) \[1\]

- **-d** INT

  retain a bubble if one side is longer than the other side by \>INT-bp \[50\]

- **-A**

  discard heterozygotes (apply this to assemble bacterial genomes; override **-O**)

- **-O**

  don't apply aggressive tip trimming

- **-g**

  output the assembly graph in the GFA format