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SIM4DBUTILS

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

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