GT-SHREDDER(1)

💖 GT-SHREDDER(1) 💖

okay bestie, welcome to the GenomeTools Manual ✨ pull up a chair, we're doing gt-shredder today 🎀

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✨ NAME ✨

gt-shredder — shredder sequence file(s) into consecutive pieces of random length 🦋

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🌸 SYNOPSIS 🌸

gt shredder [option ...] [sequence_file ...]

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💅 DESCRIPTION 💅

okay so here's the whole vibe. every flag, every default, no cap:

• -coverage [value] — set the number of times the sequence_file is shreddered (default: 1)
• -minlength [value] — set the minimum length of the shreddered fragments (default: 300)
• -maxlength [value] — set the maximum length of the shreddered fragments (default: 700)
• -overlap [value] — set the overlap between consecutive pieces (default: 0)
• -sample [value] — take samples of the generated sequences pieces with the given probability (default: 1.000000)
• -clipdesc [yes|no] — clip descriptions after first space (fooled by \t, \n etc) adds offset and length to ensure unique identifier (default: no)
• -width [value] — set output width for FASTA sequence printing (0 disables formatting) (default: 0)
• -o [filename] — redirect output to specified file (default: undefined)
• -gzip [yes|no] — write gzip compressed output file (default: no)
• -bzip2 [yes|no] — write bzip2 compressed output file (default: no)
• -force [yes|no] — force writing to output file (default: no)
• -help — display help and exit
• -version — display version information and exit

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so the tea is this 🫖: each sequence you hand over in sequence_file gets shreddered into consecutive pieces of random length (somewhere between -minlength and -maxlength) until it is fully consumed. which means — and listen, this is the important part — the last shreddered fragment of a given sequence can be shorter than the argument to option -minlength 😭 it's just how the math shakes out. if those scraggly little leftovers are giving you the ick, use gt seqfilter to get rid of them (there's an example down below, i got you 💖).

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🌈 EXAMPLES: 🌈

Shredder a given BAC:

$ gt shredder U89959_genomic.fas > fragments.fas

Shredder an EST collection into pieces between 50 and 100 bp and get rid of all (terminal) fragments shorter than 50 bp:

$ gt shredder -minlength 50 -maxlength 100 U89959_ests.fas \
  | gt seqfilter -minlength 50 - > fragments.fas
# 130 out of 1260 sequences have been removed (10.317%)

Shredder an EST collection and show only random 10% of the resulting fragments:

$ gt shredder -sample 0.1 U89959_ests.fas

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🫶 REPORTING BUGS 🫶

found a bug? not the vibe, we gotta know. report bugs to https://github.com/genometools/genometools/issues 📮

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friendly reminder bestie: this is the GenomeTools 1.6.6 release, dated 11/09/2025 🎀 so if you're reading this in some distant future era, hi, hope the shredder still slays 💜

go forth and shred, main character 🦋✨👑