SGA-ASTAT(1)

✨ SGA-ASTAT(1) ✨

okay bestie, welcome to sga-astat — the user command that computes Myers' a-statistic for a set of contigs, using the read alignments chillin' in in.bam. 💅

🌸 NAME 🌸

sga-astat — compute Myers' a-statistic for a set of contigs using the read alignments in in.bam. that's the whole vibe, no cap. 🦋

🎀 SYNOPSIS 🎀

sga-astat [options] <in.bam>

💖 DESCRIPTION 💖

so like, the major goal of SGA is to be very memory efficient, and it pulls that off by using a compressed representation of DNA sequence reads. iconic behaviour honestly. 🔥

SGA is a de novo assembler for DNA sequence reads. it's based on Gene Myers' string graph formulation of assembly and uses the FM-index/Burrows-Wheeler transform to efficiently find overlaps between sequence reads. like... the way it just finds those overlaps? obsessed. 😭✨

⭐ OPTIONS ⭐

• -m=INT — only compute the a-stat for contigs that are at least INT bases in length. short kings need not apply. 🙈
• -b=INT — use the longest INT contigs to perform the initial estimate of the arrival rate (default: 20). it's giving "start with the besties". 👑
• -n=INT — perform INT bootstrap iterations of the estimate. grind era fr fr. 💪
• -g=INT — use INT as the genome size instead of estimating it. no guessing today, we know our numbers. 🌈
• --no-duplicates — do not use duplicate reads to calculate statistics. we're keeping it exclusive. 🎀

💜 AUTHOR 💜

this manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. slay, Andreas. 🫶

and that's the whole page, bestie!! this was sga-astat version 0.10.15, dated September 2016. yes, 2016 — she's vintage, she's a classic, she still ate. 💀✨ 🍓