SGA(1)

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

✨ SGA ✨

okay so bestie, welcome to sga, aka the String Graph Assembler — it's a de novo genome assembler and it does its whole thing using string graphs 🧬💖 the manual name is SGA(1) and yes she's a User Commands girlie, main character energy fr fr.

🌸 SYNOPSIS 🌸

sga <command> [options]

that's it. that's the whole vibe. you pick a command, you hand her some options, she goes off 👑

🎀 DESCRIPTION 🎀

Program: sga Version: 0.10.15 Contact: Jared Simpson [js18@sanger.ac.uk]

so real talk, here's the whole roster of commands she's packing 👇

💅 Commands

  • preprocess — filter and quality-trim reads. the lil glow-up your reads get before anything else ✨
  • index — build the BWT and FM-index for a set of reads 📚
  • merge — merge multiple BWT/FM-index files into a single index. combine, don't divide 🫶
  • bwt2fa — transform a bwt back into a set of sequences. reverse uno card 🔄
  • correct — correct sequencing errors in a set of reads. fixing her mistakes, we love growth 😭
  • fm-merge — merge unambiguously overlapped sequences using the FM-index 🧩
  • overlap — compute overlaps between reads. the way she finds who matches with who... matchmaker energy 💖
  • assemble — generate contigs from an assembly graph. the whole point, the moment, the finale 🎆
  • oview — view overlap alignments. window shopping but for alignments 👀
  • subgraph — extract a subgraph from a graph ✂️
  • filter — remove reads from a data set 🧹
  • rmdup — duplicate read removal. no copycats allowed 🙅
  • gen-ssa — generate a sampled suffix array for the given set of reads 🧚
  • scaffold — generate ordered sets of contigs using distance estimates 🏗️
  • scaffold2fasta — convert the output of the scaffold subprogram into a fasta file 🎁
  • gapfill — fill intra-scaffold gaps 🩹

🧬 Variant Calling Commands

  • graph-diff — compare reads to find sequence variants 🔍
  • graph-concordance — check called variants for representation in the assembly graph ✅
  • rewrite-evidence-bam — fill in sequence and quality information for a variant evidence BAM 📝
  • haplotype-filter — filter out low-quality haplotypes 🚮
  • somatic-variant-filters — filter out low-quality variants 🚮🚮

🔬 Experimental commands

ngl these are the experimental girlies — they're in the lab, being studied, pls be nice to them 🧪🙈
  • preqc — perform pre-assembly quality checks on a set of reads 🔎
  • stats — print summary statistics about a read set 📊
  • filterBAM — filter out contaminating mate-pair data in a BAM file 🧼
  • cluster — find clusters of reads belonging to the same connected component in an assembly graph 🫂
  • kmer-count — extract all kmers from a BWT file 🔡

😤 REPORTING BUGS 😤

found a bug? spill the tea to js18@sanger.ac.uk — she wants to know fr fr 📧

and that's the page bestie 💜 sga 0.10.15, all the way from November 2022 — go assemble something iconic, you got this 👑✨🦋

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