---
name: "lamassemble"
section: "1"
platform: "linux"
package: "lamassemble"
version: "1.7.2-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/lamassemble"
---

# lamassemble(1)

Merges overlapping "long" DNA reads into a consensus sequences

## 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)