.TH SPRAI 1 "June 2016"
.SH NAME
SPRAI \- single-pass nucleotide sequencing read accuracy improvement
.SH SYNOPSIS
.B ezez_vx1
.I ec.spec
.RI { asm.spec \0|
.BR -ec_only }
.RI [ options ]
.br
.B ezez4qsub_vx1
.I ec.spec
.RI { asm.spec \0|
.BR -ec_only }
.RI [ options ]
.br
.B ezez4makefile_v4.pl
.I ec.spec
.RI [ asm.spec ]
&& make
.BI -j nproc
.RI [ ec_only ]
.SH 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.
.SH OPTIONS
.TP
.B \-n
Show parameters in
.I ec.spec
and exit.
.TP
.B \-ec_only
Perform error correction only.
With this option,
.I asm.spec
does not need to be passed in, as assembly is not performed.
.TP
.BI \-now \0yyyymmdd_hhmmss
Use an existing
.RI result _yyyymmdd_hhmmss
directory from a previous run, detect unfinished jobs, and restart at the appropriate stage.
.SH SEE ALSO
.BR bash5tools (1)
.br
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