KTIMPORTBLAST(1)

🦋 ktImportBLAST — bestie edition

okay so ktImportBLAST is a User Commands girlie (section 1 of the manual, she's that icon) and she's here to make your metagenomic data look ✨gorgeous✨. Buckle up, this is gonna be fun.

✨ NAME ✨

ktImportBLAST — explore hierarchical metagenomic data with zoomable pie charts 💖

🌸 DESCRIPTION 🌸

She creates a Krona chart of taxonomic classifications computed from tabular BLAST results. no cap, that's the whole vibe.

Here's how you call her:

ktImportBLAST \

       [options] \ blast_output_1[:magnitudes_1][,name_1] \
       [blast_output_2[:magnitudes_2][,name_2]] \ ...

🎀 the arguments (aka what you're actually feeding her)

• blast_output — a file with your BLAST results in tabular format (that's the "Hit table (text)" option when you download from NCBI, iykyk). If you're running BLAST locally, the subject IDs in your local database must contain accession numbers, either bare or sitting in the fourth field of that pipe-separated format: "gi|12345|xx|ABC123.1|". By default, she makes separate datasets for each input — see [-c] if you want to change that 💅
• magnitudes — optional file listing query IDs with magnitudes, separated by tabs 🫶 This one's for accounting for read length or contig depth so you get a way more accurate picture of abundance. By default, query sequences with no specified magnitudes get a magnitude of 1. And psst — magnitude files for assemblies in ACE format can be made with ktGetContigMagnitudes.
• name — a name to show in the list of datasets in the Krona chart (this matters when you have multiple input files and [-c] is not specified). By default she just uses the basename of the file. lowkey efficient.

💅 OPTIONS 💅

one bullet per option, because we keep every single one. no skipping, no summarising, that's the rules.

• -o <string> — output file name. [Default: 'blast.krona.html'] 💾
• -n <string> — name of the highest level. [Default: 'Root'] 🌳
• -t <number> — threshold for bit score differences when figuring out the "best" hits. Hits with scores within this distance of the highest score get included when computing the lowest common ancestor (or picked randomly if -r is specified). [Default: '3'] 🔥
• -i — include a wedge for queries that got no hits. gotta represent the empty girls too 🙈
• -f — if any best hits have unknown accessions, force classification to root instead of just ignoring them. 💀
• -r — pick from the best hits randomly instead of finding the lowest common ancestor. chaos mode, love that for you 🎲
• -p — use percent identity for average scores instead of log[10] e-value. 💯
• -b — use bit score for average scores instead of log[10] e-value. ⭐
• -c — combine data from each file, rather than creating separate datasets within the chart. all together now 🫂
• -d <integer> — maximum depth of wedges to include in the chart. 📏
• -k — show the "cellular organisms" taxon (she's collapsed by default, so this un-collapses her). 🦠
• -K — collapse assignments to taxa with ranks labeled "no rank" by moving up to the parent. 🧚
• -x <integer> — hue (0-360) for "bad" scores. [Default: '0'] 👎
• -y <integer> — hue (0-360) for "good" scores. [Default: '120'] 👍
• -u <string> — URL of Krona resources to use instead of bundling them with the chart (e.g. "http://krona.sourceforge.net"). It reduces the size of charts and allows updates, though — heads up — charts will not work without access to this URL. ⚠️
• -qp <string> — url to send query IDs to (instead of listing them) for each wedge. The query IDs get sent as a comma separated list in the POST variable "queries", with the current dataset index (from 0) in the POST variable "dataset". The url can include additional variables encoded via GET. 📮
• -tax <string> — path to the directory containing a taxonomy database to use. [Default: '/usr/share/perl5/KronaTools/taxonomy'] 🗂️
• -e <number> — e-value factor for determining "best" hits. real talk: a bit score difference threshold (-t) is recommended instead, to avoid comparing e-values that BLAST reports as 0 due to floating point underflow. However, an e-value factor should be used if the input is a concatenation of BLASTs against different databases. so, context-dependent, bestie 🧠

not me writing a whole manual page and every single option still being in here 💀 the way that consistency is the moment. periodt.

and that's the whole page!! 🎀 written by the KronaTools girlies, version 2.8, dated June 2021 — slay, bye, go make some pie charts 💖✨🦋