SALMON_INDEX(1)

📦
version 1.10.3 · 5 versions
, in ubuntu resolute, ubuntu stonking

💖 SALMON_INDEX 💖

okay bestie, welcome to SALMON_INDEX(1) — that's the User Commands section of the manual, and yes it's exactly as iconic as it sounds 💅

🌸 NAME 🌸

salmon_index — highly-accurate, transcript-level quantification estimates from RNA-seq data 🧬✨

🦋 DESCRIPTION 🦋

📦 Index

Creates a salmon index. That's it, that's the whole vibe — it builds the index, no cap. 🫶

✨ Command Line Options ✨

okay so here's the full menu, every single one, we're not skipping a thing 🎀

  • -v, --version — print version string. just flexes the version number at you 💁‍♀️
  • -h, --help — produce help message. the classic "help me help you" move 🙈
  • -t, --transcripts arg — Transcript fasta file. this is your input bestie, the transcripts themselves 🌈
  • -k, --kmerLen arg (=31) — The size of k-mers that should be used for the quasi index. default is 31 and it's giving very much "trust the defaults" ⭐
  • -i, --index arg — salmon index. (yes, that's the whole description. it's the index. slay.) 👑
  • --gencode — This flag will expect the input transcript fasta to be in GENCODE format, and will split the transcript name at the first | character. These reduced names will be used in the output and when looking for these transcripts in a gene to transcript GTF. so basically it chops the name at the first pipe and rolls with the short version ✂️
  • --features — This flag will expect the input reference to be in the tsv file format, and will split the feature name at the first 'tab' character. These reduced names will be used in the output and when looking for the sequence of the features.GTF. same energy as above but it's a tsv and it's splitting on the first tab 🍓
  • --keepDuplicates — This flag will disable the default indexing behavior of discarding sequence-identical duplicate transcripts. If this flag is passed, then duplicate transcripts that appear in the input will be retained and quantified separately. so default = bye bye duplicates, this flag = okay actually stay, and they get quantified separately 💀
  • -p, --threads arg (=2) — Number of threads to use during indexing. default is 2, crank it up if you're impatient 🔥
  • --keepFixedFasta — Retain the fixed fasta file (without short transcripts and duplicates, clipped, etc.) generated during indexing. it keeps the tidy-up version around for you 💖
  • -f, --filterSize arg (=-1) — The size of the Bloom filter that will be used by TwoPaCo during indexing. The filter will be of size 2^{filterSize}. The default value of -1 means that the filter size will be automatically set based on the number of distinct k-mers in the input, as estimated by nthll. so -1 is the "just figure it out for me" setting and honestly, respect 🧚
  • --tmpdir arg — The directory location that will be used for TwoPaCo temporary files; it will be created if need be and be removed prior to indexing completion. The default value will cause a (temporary) subdirectory of the salmon index directory to be used for this purpose. so if you don't say anything, it makes its own lil temp spot inside the salmon index dir and cleans up after itself 🧹✨
  • --sparse — Build the index using a sparse sampling of k-mer positions. This will require less memory (especially during quantification), but will take longer to construct and can slow down mapping / alignment. tradeoff alert 🚨 less memory, more waiting, slower mapping/alignment — pick your fighter ⚖️
  • -d, --decoys arg — Treat these sequences ids from the reference as the decoys that may have sequence homologous to some known transcript. for example in case of the genome, provide a list of chromosome name --- one per line. one chromosome name per line, bestie, don't smoosh them together 📝
  • -n, --no-clip — Don't clip poly-A tails from the ends of target sequences. the poly-A tails get to stay, untouched, unbothered 🌸
  • --type arg (=puff) — The type of index to build; the only option is "puff" in this version of salmon. one option, one legend, "puff" periodt ☁️
heads up bestie: this is the whole page — no SEE ALSO, no bugs section, no authors listed, nothing hiding at the bottom. we covered every flag, every default, every argument. you're fully caught up 💅

and that's the whole thing!! this page came from the User Commands manual, it's dated February 2026, and the footer tag was doing its lil thing with salmon --no-version-check ind... — which like, iconic cryptic energy honestly 😭

it all lives under SALMON_INDEX(1) and you're gonna go build a gorgeous index now. go off 👑💖✨

📦 where this page comes from