SIM4DBUTILS(1)

✨ SIM4DBUTILS ✨

okay so welcome to sim4dbutils, bestie 💖 — a whole lil squad of utilities for working with alignment files that sim4db(1) made. This one lives in the General Commands Manual, and it's literally a grab-bag of tools, so let's get into it 🎀

🌸 NAME 🌸

sim4dbutils — utilities to work with sim4db-generated alignment files 🦋

here's the whole lineup, no gatekeeping:

• 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 💀

these ones are giving legacy energy, iykyk:

• 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. periodt 💜

🎀 SEE ALSO 🎀

• sim4db(1)
• http://kmer.sourceforge.net/wiki/index.php/Sim4db_Files

okay that's the whole page, bestie, you ate 🫶 this was the SIM4DBUTILS(1) page from the General Commands Manual, dated January 2016 — iconic, lowkey vintage, and now it's yours 💖✨