sga(1)

sga1

String graph assembler: de novo genome assembler that uses string graphs

Usage

sga <command> [options]

Overview

Program: sga Version: 0.10.15 Contact: Jared Simpson [[email protected]]

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

Releases

5 releases since Debian 9 (Stretch); the text changed 3 times.