NAME

       sim4dbutils - utilities to work with sim4db-generated alignment files

       convertPolishes - convert between sim4db and GFF3 formats
       filterPolishes - filter alignments based on sequence identity, coverage and length.
       mergePolishes - merge alignments from multiple files
       sortPolishes - sort alignments by cDNA or genomic sequence index or sequence name
       convertToExtent - Convert from sim4db format to a single-line tab-delimited format
       fixPolishesIID - Updates a sim4db file to use the sequence index of a specific fasta file.
       Can also be used to extract a subset of the alignments from the sim4db file.
       depthOfPolishes - Outputs a tab-delimited histogram of the depth of  polishes  at  various
       window sizes.
       headPolishes - print the first N alignments in a file, similar to head(1)
       pickBestPolish - report only the 'best' alignment for each cDNA
       pickUniquePolish  -  reports  alignments  where there is a clear single best alignment for
       each cDNA.
       plotCoverageVsIdentity - Generates  (1)  a  histogram  of  the  percent  identity,  (2)  a
       histogram  of  the  percent coverage, and (3) a list of percent identity and coverage (for
       use in a scatter plot).
       uniqPolishes - Filters out all alignments for cDNA with  multiple  alignments  (-uniq)  or
       with a single alignment (-dupl). Similar to uniq(1)
       realignPolishes - recompute the alignments listed in a sim4db file.
       reportAlignmentDifferences  -  generates  a  histogram  of the types of errors in a set of
       alignments Unsupported and Deprecated
       comparePolishes - Correlate alignments in two files.
       convertToAtac - Converts from sim4db format to ATAC format.
       detectChimera - Examines alignments for sequences that might be chimeric.
       mappedCoverage - Reports the amount of the query sequence (EST, cDNA) that is  covered  by
       alignments.
       parseSNP - Analyzes alignments for SNPs.
       removeDuplicate - searches the input for duplicate alignments.
       vennPolishes  -  Generates  a  Venn diagram for multiple sim4db files.  Used internally by
       ESTMapper cleanPolishes
       summarizePolishes

DESCRIPTION

       These programs are a range of utilities to work with sim4db(1)-generated alignment files.

SEE ALSO

       sim4db(1),
       http://kmer.sourceforge.net/wiki/index.php/Sim4db_Files

                                           January 2016                            SIM4DBUTILS(1)