SNAP-ALIGNER_INDEX(1)

💖 SNAP-ALIGNER_INDEX 💖

okay bestie, gather round, because this is the snap-aligner_index page — it's part of SNAP, the scalable nucleotide alignment program, and it lives in the User Commands corner of your manual. it builds indices. it's iconic. let's go 🧚

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✨ SYNOPSIS ✨

snap-aligner index <input.fa> <output-dir> [<options>]

that's the whole vibe: you hand it a FASTA, you tell it where to put the output, and then you sprinkle options on top like glitter 🎀

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🌸 DESCRIPTION 🌸

hiii, welcome to SNAP version 2.0.5 💅 no cap, that's literally the entire description. short and sweet, main character energy.

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👑 OPTIONS 👑

• -s — the seed size. default is 24. 🌱
• -h — hash table slack. default is 0.3. lowkey important, highkey vibes.
• -t — how many threads max you wanna use. default is the number of cores you've got. ⚠️ do not put a space after the -t, like, at all — it's -t16, not -t 16. the way that it just wants them glued together, fr fr.
• -B<chars> — tells it which characters count as chromosome name terminators in the FASTA header line. those characters and everything after them are not part of the chromosome name. and listen: you have to put all the characters on a single -B switch. so for example, with -B_|, a FASTA header line like >chr1|Chromosome 1 would generate a chromosome named chr1. slay. ✨ there's a separate flag for saying a space is a terminator (see -bSpace below).
• -bSpace — says that the space and tab characters are terminators for chromosome names (see -B above). you can use this in addition to other terminators you set with -B. -B and -bSpace are both case sensitive. this is the default. 🫶
• -bSpace- — says that space and tab characters should be included in chromosome names. opposite day, but make it useful.
• -p — how many Ns to put as padding between chromosomes. it must be as large as the largest edit distance you'll ever use, and there's a performance advantage to making it bigger than any read you'll process or any gap between paired-end reads. default is 2000. write the padding amount directly after -p, no space. 💀
• -H — build a histogram of seed popularity. this is just for information, it is not used by SNAP. put the histogram file name directly after -H with no space. 📊
• -exact — compute hash table sizes exactly. this will slow down the index build, but usually results in smaller indices. small sacrifice, big payoff. 💜
• -keysize — the number of bytes to use for the hash table key. bigger values bump up SNAP's memory footprint but let you have larger seeds. by default it's autoselected based on the seed size. 🔑
• -large — builds a larger index that's a little faster, especially for runs with quick/inaccurate parameters. increases index size by about 30%, depending on the other index parameters and the contents of the reference genome. 🌈
• -locationSize — the size of the genome locations stored in the index. this can be from 4 to 8 bytes. the locations need to be big enough not only to index the genome, but also to leave some room for representing seeds that occur multiple times. for the human genome, four byte locations fit if the seed size is 20 or larger, but you need 5 (or more) for smaller seeds. making the location size bigger than necessary will just waste (lots of) space, so unless you're doing something quite unusual, the right answer is 4 or 5. default is based on seed size: 4 if it's 20 or greater, 5 otherwise. 📍
• -sm — use a temp file so it works better in smaller memory. this only helps a little, but it can be the difference if you're close. specifically, this will generally use less memory than the index will use once it's built, so if this doesn't work you won't be able to use the index anyway. however, if you've already got sufficient memory to begin with, this option will just slow down the index build by doing extra, useless IO. 😭
• -AutoAlt- — don't automatically mark ALT contigs. otherwise, any contig whose name ends in _alt (regardless of capitalization) or starts with HLA- will be marked ALT. others will not. 🙈
• -maxAltContigSize — specify a size at or below which all contigs are automatically marked ALT, unless overridden by name using the args below. 📏
• -altContigName — specify the (case independent) name of an alt to mark a contig. you can supply this parameter as often as you'd like. 🔁
• -altContigFile — specify the name of a file with a list of alt contig names, one per line. you may specify this as often as you'd like. 📄
• -nonAltContigName — specify the name of a contig that's not an alt, regardless of its size. 🚫
• -nonAltContigFile — specify the name of a file that contains a list of contigs (one per line) that will not be marked ALT regardless of size. 📃
• -altLiftoverFile — specify the file containing ALT-to-REF mappings (SAM format). e.g., hs38DH.fa.alt from bwa-kit. 🔥
• -q — quiet mode: don't print status messages (other than the welcome message, which gets printed prior to parsing args). error messages are still printed. 🤫
• -qq — super quiet mode: don't print status or error messages. maximum silence, maximum mystery. 💀

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heads up bestie: some of these switches are fussy about spacing (-t, -p, -H want their values glued on with no space), and -B / -bSpace are case sensitive. read before you type, iykyk. 🫶

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okay and that's a wrap on the page 🎀 it's snap-aligner index version 2.0.5, dated September 2025 — go build something gorgeous, bestie, you've got this 💅✨🦋