| SIM4DBUTILS(1) | General Commands Manual | SIM4DBUTILS(1) |
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
These programs are a range of utilities to work with sim4db(1)-generated alignment files.
sim4db(1),
http://kmer.sourceforge.net/wiki/index.php/Sim4db_Files
| January 2016 |