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)