Provided by: sim4db_0~20150903+r2013-6_amd64
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 SIM4DBUTILS(1)