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sim4dbutils - utilities to work with sim4db-generated alignment files

SIM4DBUTILS(1) General Commands Manual SIM4DBUTILS(1)

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 Debian Sid