---
name: "ssake"
section: "1"
platform: "linux"
package: "ssake"
version: "4.0.1-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/ssake"
---

# ssake(1)

assembling millions of very short DNA sequences

## NAME

ssake - assembling millions of very short DNA sequences

## SYNOPSIS

Progressive assembly of millions of short DNA sequences by k-mer search through a prefix tree and 3' extension.

## OPTIONS

- \-f

  Fasta file containing all the \[paired (-p 1) / unpaired (-p 0)\] reads (required) **paired reads must now be separated by ":"**

- \-s

  Fasta file containing sequences to use as seeds exclusively (specify only if different from read set, optional)

- \-m

  Minimum number of overlapping bases with the seed/contig during overhang consensus build up (default -m 16)

- \-o

  Minimum number of reads needed to call a base during an extension (default -o 3)

- \-r

  Minimum base ratio used to accept a overhang consensus base (default -r 0.7)

- \-t

  Trim up to -t base(s) on the contig end when all possibilities have been exhausted for an extension (default -t 0)\>

- \-p

  Paired-end reads used? (-p 1=yes, -p 0=no, default -p 0)

- \-v

  Runs in verbose mode (-v 1=yes, -v 0=no, default -v 0, optional)

- \-b

  Base name for your output files (optional)

\============ Options below only considered with -p 1 ============

- \-d

  Mean distance expected/observed between paired-end reads (default -d 200, optional)

- \-e

  Error (%) allowed on mean distance   e.g. -e 0.75  == distance +/- 75% (default -e 0.75, optional)

- \-k

  Minimum number of links (read pairs) to compute scaffold (default -k 2, optional)

- \-a

  Maximum link ratio between two best contig pairs \*higher values lead to least accurate scaffolding\* (default -a 0.70, optional)

- \-z

  Minimum contig size to track paired-end reads (default -z 50, optional)

- \-g

  Fasta file containing unpaired sequence reads (optional)

## SEE ALSO

/usr/share/doc/ssake/SSAKE.readme between

## AUTHORS

This manual page was written by Andreas Tille \<tille@debian.org\> for the **Debian** system (but may be used by others).  Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by the Free Software Foundation.

On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.