GTHCONSENSUS(1)

✨ GTHCONSENSUS 💅

okay so bestie, welcome to gthconsensus — section 1 of the manual, she's a command-line girlie and she's about to make your spliced alignments agree with each other. 🫶

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🌸 NAME 🌸

gthconsensus — build consensus spliced alignments

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🎀 SYNOPSIS 🎀

gthconsensus [option ...] [file ...]

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🦋 DESCRIPTION 🦋

So here's the vibe: you show gthconsensus a bunch of GenomeThreader output files that are holding intermediate results, and she takes all the spliced alignments chilling inside them and assembles them into consensus spliced alignments. That's it, that's the whole job. Group project, but she does the merging. 👑

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✨ OPTIONS ✨

• -translationtable — sets the codon translation table used for codon translation in matching, DP, and output. default: 1
• -v — be verbose. default: no
• -xmlout — show output in XML format. default: no
• -gff3out — show output in GFF3 format. default: no
• -md5ids — show MD5 fingerprints as sequence IDs. default: no
• -o — redirect output to specified file. default: undefined
• -gzip — write gzip compressed output file. default: no
• -bzip2 — write bzip2 compressed output file. default: no
• -force — force writing to output file. default: no
• -gs2out — output in old GeneSeqer2 format. default: no
• -minalignmentscore — set the minimum alignment score for spliced alignments to be included into the set of spliced alignments. default: 0.00
• -maxalignmentscore — set the maximum alignment score for spliced alignments to be included into the set of spliced alignments. default: 1.00
• -mincoverage — set the minimum coverage for spliced alignments to be included into the set of spliced alignments. default: 0.00
• -maxcoverage — set the maximum coverage for spliced alignments to be included into the set of spliced alignments. default: 9999.99
• -intermediate — stop after calculation of spliced alignments and output results in reusable XML format. Do not process this output yourself, use the ``normal'' XML output instead! default: no

🚨 bestie listen to me on this one — that -intermediate XML is not for you to go poking at with your own little scripts. Use the "normal" XML output instead, fr fr. she said what she said. 💀

• -help — display help for basic options and exit
• -help+ — display help for all options and exit
• -version — display version information and exit

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and that's the whole page, periodt 💖 this little icon lives in the GTHCONSENSUS(1) manual, section 1, and she signs off the same way she showed up — same name, top and bottom, no notes. go build some consensus alignments, you absolute main character. 🧚✨👑