---
name: "sprai"
section: "1"
platform: "linux"
package: "sprai"
version: "0.9.9.23+dfsg1-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/sprai"
---

# sprai(1)

single-pass nucleotide sequencing read accuracy improvement

## NAME

SPRAI - single-pass nucleotide sequencing read accuracy improvement

## SYNOPSIS

**ezez\_vx1** *ec.spec* {*asm.spec* \| **-ec\_only**} \[*options*\]\
 **ezez4qsub\_vx1** *ec.spec* {*asm.spec* \| **-ec\_only**} \[*options*\]\
 **ezez4makefile\_v4.pl** *ec.spec* \[*asm.spec*\] && make **-j***nproc* \[*ec\_only*\]

## DESCRIPTION

Sprai is a tool to correct sequencing errors in single-pass reads for de novo assembly. It is originally designed for correcting sequencing errors in single-molecule DNA sequencing reads, especially in Continuous Long Reads (CLRs) generated by PacBio RS sequencers. The goal of Sprai is not maximizing the accuracy of error-corrected reads. Instead, Sprai aims at maximizing the continuity (i.e., N50 contig length) of assembled contigs after error correction.

## OPTIONS

- **-n**

  Show parameters in *ec.spec* and exit.

- **-ec\_only**

  Perform error correction only. With this option, *asm.spec* does not need to be passed in, as assembly is not performed.

- **-now** *yyyymmdd\_hhmmss*

  Use an existing result*\_yyyymmdd\_hhmmss* directory from a previous run, detect unfinished jobs, and restart at the appropriate stage.

## SEE ALSO

[**bash5tools**(1)](/bash5tools/1.md)\
 This program is part of sprai. See the sprai package documentation in /usr/share/doc/sprai, especially the example ec and pbasm spec files in /usr/share/doc/sprai/examples