---
name: "sga"
section: "1"
platform: "linux"
package: "sga"
version: "0.10.15-7+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/sga"
---

# sga(1)

String Graph Assembler: de novo genome assembler that uses string graphs

## NAME

sga - String Graph Assembler: de novo genome assembler that uses string graphs

## SYNOPSIS

**sga** *\<command\>* \[*options*\]

## DESCRIPTION

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

### Commands:

- preprocess

  filter and quality-trim reads

- index

  build the BWT and FM-index for a set of reads

- merge

  merge multiple BWT/FM-index files into a single index

- bwt2fa

  transform a bwt back into a set of sequences

- correct

  correct sequencing errors in a set of reads

- fm-merge

  merge unambiguously overlapped sequences using the FM-index

- overlap

  compute overlaps between reads

- assemble

  generate contigs from an assembly graph

- oview

  view overlap alignments

- subgraph

  extract a subgraph from a graph

- filter

  remove reads from a data set

- rmdup

  duplicate read removal

- 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:

- 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

Report bugs to js18@sanger.ac.uk