CHIMERASLAYER(1)

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✨ CHIMERASLAYER ✨

okay bestie, welcome to chimeraslayer(1) — it's in the User Commands section of the manual, and it's literally about hunting down chimeras. no, not the mythological ones 💀 the DNA kind. let's get into it 🧚

💖 NAME 💖

chimeraslayer — detects likely chimeras in PCR amplified DNA 🔍🧬

🌸 DESCRIPTION 🌸

ChimeraSlayer is a chimeric sequence detection utility, and the way it just works for both near-full length Sanger sequences and shorter 454-FLX sequences (~500bp)? iconic. versatile. she does it all 💅

Chimera Slayer runs a whole lil series of steps that operate to flag chimeric 16S rRNA sequences, and honestly the pipeline is giving main character energy:

  1. the ends of a query sequence are searched against an included database of reference chimera-free 16S sequences to identify potential parents of a chimera 👀
  2. candidate parents of a chimera are selected as those that form a branched best scoring alignment to the NAST-formatted query sequence
  3. the NAST alignment of the query sequence is improved in a ‘chimera-aware’ profile-based NAST realignment to the selected reference parent sequences ✨
  4. an evolutionary framework is used to flag query sequences found to exhibit greater sequence homology to an in silico chimera formed between any two of the selected reference parent sequences 🚩
heads up bestie: to run Chimera Slayer, you need NAST-formatted sequences generated by the nast-ier utility. no nast-ier, no slaying. periodt.

ChimeraSlayer is part of the microbiomeutil suite. 🫶

🎀 OPTIONS 🎀

💜 Required

  • --query_NAST — multi-fasta file containing query sequences in alignment format. this one is not optional, she's the moment 🫶

🌈 Common options

  • --db_NAST — db in NAST format (default: /usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta)
  • --db_FASTA — db in fasta format (megablast formatted) (default: /usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta)
  • -n — number of top matching database sequences to compare to (default 15)
  • -R — min divergence ratio default: 1.007
  • -P — min percent identity among matching sequences (default 90)

🧬 Parameters to tune ChimeraParentSelector:

Scoring parameters, bestie — this is where you dial in the vibe:

  • -M — match score (default: +5)
  • -N — mismatch penalty (default: -4)
  • -Q — min query coverage by matching database sequence (default 70)
  • -T — maximum traverses of the multiple alignment (default 1)

🔥 Parameters to tune ChimeraPhyloChecker

  • --windowSize — default 50
  • --windowStep — default 5
  • --minBS — minimum bootstrap support for calling chimera (default 90)
  • --num_BS_replicates — default: 100
  • --low_range_finer_BS — (default: 10) If computed BS is between minBS and (minBS - low_range_finer_BS), then num_finer_BS_replicates computed.
  • --num_finer_BS_replicates — (default: 1000)
  • -S — percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10)
  • --num_parents_test — number of potential parents to test for chimeras (default 3)
  • --MAX_CHIMERA_PARENT_PER_ID — Chimera/Parent alignments with perID above this are considered non-chimeras (default 100; turned off)

🍓 Misc options

  • --printFinalAlignments — shows alignment between query sequence and pair of candidate chimera parents
  • --printCSalignments — print ChimeraSlayer alignments in ChimeraSlayer output
  • --exec_dir — chdir to here before running

🦋 SEE ALSO 🦋

👑 AUTHOR 👑

This manual page was written by Andreas Tille <tille@debian.org> but can be freely used for any other distribution. slay, Andreas, we love a permissive license 💖

and that's the whole page, bestie!! this one's chimeraslayer, dated June 2013, and it lives right back where we started under the CHIMERASLAYER(1) header. go forth and de-chimera your reads ✨🧬💅

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