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PROGRAM:
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.
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