SPLAZERS(1)

💖 SPLAZERS(1) 💖

okay bestie, sit DOWN, because this is splazers, aka Split-map read sequences, and she is serving prefix-suffix mapping realness. 🌸 This is the SPLAZERS(1) manual, and yes, I'm gonna walk you through every single flag because you deserve the full ✨experience✨, not the cliffnotes.

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✨ NAME ✨

splazers — Split-map read sequences 🦋

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✨ SYNOPSIS ✨

splazers [OPTIONS] <GENOME FILE> <READS FILE>
splazers [OPTIONS] <GENOME FILE> <READS FILE 1> <READS FILE 2>

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✨ DESCRIPTION ✨

So here's the tea, bestie 🍓: splazers uses a prefix-suffix mapping strategy to split-map read sequences.

If you hand her a SAM file of mapped reads as input, then all the unmapped-but-anchored reads get split-mapped onto anchoring target regions — and for that you gotta specify option -an, okay? Don't forget it. 👑

If instead you hand her a Fasta/q file of reads, then reads get split-mapped onto the whole reference sequence. Rainbow energy. 🌈

(c) Copyright 2010 by Anne-Katrin Emde.

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✨ REQUIRED ARGUMENTS ✨

ARGUMENT 0 INPUT_FILE

A reference genome file. The valid filetypes are .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .fas[.*], .faa[.*], .fa[.*], .embl[.*], and .bam — and where that * shows up, it can be any of these extensions: gz, bz2, and bgzf for transparent (de)compression. So yeah, she'll unzip your stuff on the fly, no cap. 💅

READS — List of INPUT_FILE's

Either one (single-end) or two (paired-end) read files. Same valid filetypes as above, literally the whole list again: .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .fas[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where * is any of gz, bz2, and bgzf for transparent (de)compression. 🎀

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✨ OPTIONS ✨

• -h, --help — Display the help message.
• --version — Display version information.

💅 Main Options::

• -o, --output OUTPUT_FILE — Change the output filename. Default: <READS FILE>.result.
• -f, --forward — only compute forward matches.
• -r, --reverse — only compute reverse complement matches.
• -i, --percent-identity DOUBLE — Percent identity threshold. In range [50..100]. Default: 92.
• -rr, --recognition-rate DOUBLE — set the percent recognition rate. In range [80..100]. Default: 99.
• -pd, --param-dir STRING — Read user-computed parameter files in the directory <DIR>.
• -id, --indels — Allow indels. Default: mismatches only.
• -ll, --library-length INTEGER — Paired-end library length. In range [1..inf]. Default: 220.
• -le, --library-error INTEGER — Paired-end library length tolerance. In range [0..inf]. Default: 50.
• -m, --max-hits INTEGER — Output only <NUM> of the best hits. In range [1..inf]. Default: 100.
• --unique — Output only unique best matches, which is literally -m 1 -dr 0 -pa.
• -tr, --trim-reads INTEGER — Trim reads to the given length. Default: off. In range [14..inf].
• -mcl, --min-clipped-len INTEGER — min. read length for read clipping. In range [1..inf]. Default: 0.
• -qih, --quality-in-header — quality string in fasta header.
• -ou, --outputUnmapped OUTPUT_FILE — output filename for unmapped reads.
• -v, --verbose — verbose mode.
• -vv, --vverbose — very verbose mode. (she's loud, she's proud 🔥)

🌈 Output Format Options::

• -a, --alignment — dump the alignment for each match.
• -pa, --purge-ambiguous — purge reads with more than max-hits best matches.
• -dr, --distance-range INTEGER — only consider matches with at most NUM more errors compared to the best (default output all).
• -of, --output-format INTEGER — Set output format. 0 = RazerS, 1 = Enhanced Fasta, 2 = Eland, 3 = GFF, 4 = SAM. In range [0..4].
• -gn, --genome-naming INTEGER — Select how genomes are named. 0 = use Fasta id, 1 = enumerate beginning with 1. In range [0..1]. Default: 0.
• -rn, --read-naming INTEGER — Select how reads are named. 0 = use Fasta id, 1 = enumerate beginning with 1. In range [0..1]. Default: 0.
• -so, --sort-order INTEGER — Select how matches are sorted. 0 = read number, 1 = genome position. In range [0..1]. Default: 0.
• -pf, --position-format INTEGER — Select begin/end position numbering (see the Coordinate section below). 0 = gap space, 1 = position space. In range [0..1]. Default: 0.

🧚 Split Mapping Options::

• -sm, --split-mapping INTEGER — min. match length for prefix/suffix mapping (to disable split mapping, set it to 0). Default: 18.
• -maxG, --max-gap INTEGER — max. length of middle gap. Default: 10000.
• -minG, --min-gap INTEGER — min. length of middle gap (for edit distance mapping about 10% of read length is recommended). Default: 0.
• -ep, --errors-prefix INTEGER — max. number of errors in prefix match. Default: 1.
• -es, --errors-suffix INTEGER — max. number of errors in suffix match. Default: 1.
• -gl, --genome-len INTEGER — genome length in Mb, for computation of the expected number of random matches. In range [-inf..10000]. Default: 3000.
• -an, --anchored — anchored split mapping: only unmapped reads with mapped mates will be considered, and it requires the reads to be given in SAM format. 👑
• -pc, --penalty-c INTEGER — percent of read length, used as penalty for split-gap. Default: 2.

🌸 Filtration Options::

• -oc, --overabundance-cut INTEGER — Set the k-mer overabundance cut ratio. In range [0..1].
• -rl, --repeat-length INTEGER — Skip simple-repeats of length <NUM>. In range [1..inf]. Default: 1000.
• -tl, --taboo-length INTEGER — Set taboo length. In range [1..inf]. Default: 1.
• -lm, --low-memory — decrease memory usage at the expense of runtime.

🦋 Verification Options:

• -mN, --match-N — N matches all other characters. Default: N matches nothing.
• -ed, --error-distr STRING — Write error distribution to FILE.

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bestie bestie bestie — remember -an needs SAM format reads and only looks at unmapped reads that have mapped mates. And --unique is literally -m 1 -dr 0 -pa in a trench coat. iykyk 💜

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and that's the whole page, no crumbs left 💅 this was splazers version 1.3.12 [tarball], from the SPLAZERS(1) manual — go split-map something iconic, mwah 🎀✨