SPRAI(1) single-pass nucleotide sequencing read accuracy improvement


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]


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.


Show parameters in ec.spec and exit.
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.