SGA-BAM2DE(1)

📦
version 0.10.15 · 4 versions
, in ubuntu noble, ubuntu questing

💖 SGA-BAM2DE(1) 💖

okay bestie, welcome to the User Commands section of the manual, this is SGA-BAM2DE(1) and she is so useful, come sit with me 🫶

✨ NAME ✨

sga-bam2de — make a distance estimate file from a bam file of reads aligned to contigs 🧬

🌸 DESCRIPTION 🌸

so basically, sga-bam2de.pl takes a bam file of reads that are aligned to contigs and it makes you a distance estimate file. that's the whole vibe. that's her job. 💅

here's how you'd actually run her:

sga-bam2de.pl -n N --prefix lib300 lib300.bam

and now the options, no cap, all of them 👇

🎀 OPTIONS 🎀

  • -n N — minimum number of pairs required before we'll consider two contigs linked. like, N pairs or it's not a link, periodt. 🔗
  • -m LEN — only find links between contigs that are at least LEN bp long. (default: 200) 📏
  • -t NUM — use NUM threads for computing the distance estimates. multitasking queen 👑
  • --prefix NAME — use NAME as the prefix for the outfiles. name your babies 🍼
  • --mind D — set the minimum distance estimate to test to be D. > heads up bestie: this should be a negative number if contigs are expected to overlap! defaults to -99bp. 🙈
  • --mina N — set the minimum alignment length to be N. ✨
  • --help — this help output. hi, that's me, you're reading me 💖

and that's the whole page, you ate that fr fr 🌈

this was sga-bam2de version 0.10.15, dated November 2022, and the manual page itself is SGA-BAM2DE(1). mwah, go read some bams 💋💜

📦 where this page comes from