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 -jnproc [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)
       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

                                                    June 2016                                           SPRAI(1)