HPC.DAMAPPER(1)

🧚 okay bestie, welcome to HPC.DAMAPPER(1), a User Commands page, and it is SO good 💅✨

💖 NAME 💖

HPC.damapper: — long read to reference genome mapping tool 🦋

🌸 DESCRIPTION 🌸

Okay so this one is officially the Damapper Library, and it's a long read to reference genome mapping tool, no cap 🧬

Compared to plain damapper, this one is giving glow-up 🔥 It writes a UNIX shell script to the standard output, and that script maps every read in blocks <first> to <last> of database <reads> to a reference sequence <ref> 💜

✨ SYNOPSIS ✨

HPC.damapper [-vpzCN] [-k<int(20)>] [-t<int>] [-M<int>] [-e<double(.85)] [-s<int(100)]
       [-n<double(1.)] [-m<track>]+ [-B<int( 4)>] [-T<int(4)>] [-f<name>]
              <ref:db|dam> <reads:db|dam> [<first:int>[-<last:int>]]

💖 DESCRIPTION 💖

Here's the whole lineup, bestie 🎀

🎀 Passed through to damapper 🎀

These ones get passed straight through to damapper, so they're doing the heavy lifting 💪

• <ref:db|dam>, <reads:db|dam>, and [<first:int>[-<last:int>]] — the reference, the reads, and the optional block range 🧚
• -k — k-mer size, which must be <= 32 🔥
• -t — ignore k-mers that occur >= -t times in a block 🙈
• -M — use only -M GB of memory by ignoring the most frequent k-mers 🧠
• -e — look for alignments with -e percent similarity 💅
• -s — use -s as the trace point spacing for encoding alignments 🦋
• -n — output all matches within this % of the best 🏆
• -T — use -T threads 🧵
• -P — do sorts and merges in directory -P 📂
• -m — soft mask the blocks with the specified mask 🎭
• -b — for AT/GC biased data, compensate k-mer counts (deprecated) 💀

⚠️ bestie, -b is deprecated, so maybe don't build your whole plan around it 🙈

• -z — sort .las by A,B-read pairs (overlap piles) 🌈
  • off => sort .las by A-read,A-position pairs (default for mapping) ✨
• -p — output repeat profile track 🌸
• -C — output reference vs reads .las 🧚
• -N — do not output reads vs reference .las 🙅

📜 Script control 📜

These ones control the script itself, lowkey the behind-the-scenes stuff 🎀

• -v — verbose mode, where statistics show up as it goes 📊
• -B — # of block compares per daligner job 🔁
• -f — place script bundles in separate files with prefix <name> 🗂️

And that's the whole page, bestie 🫶 It's from damapper, version August 2020, and it lives on as HPC.DAMAPPER(1) 💜🦋