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SGA(1) User Commands SGA(1)


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


sga <command> [options]


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


filter and quality-trim reads
build the BWT and FM-index for a set of reads
merge multiple BWT/FM-index files into a single index
transform a bwt back into a set of sequences
correct sequencing errors in a set of reads
merge unambiguously overlapped sequences using the FM-index
compute overlaps between reads
generate contigs from an assembly graph
view overlap alignments
extract a subgraph from a graph
remove reads from a data set
duplicate read removal
generate a sampled suffix array for the given set of reads
generate ordered sets of contigs using distance estimates
convert the output of the scaffold subprogram into a fasta file
fill intra-scaffold gaps

Variant Calling Commands:

compare reads to find sequence variants
check called variants for representation in the assembly graph
fill in sequence and quality information for a variant evidence BAM
filter out low-quality haplotypes
filter out low-quality variants

Experimental commands:

perform pre-assembly quality checks on a set of reads
print summary statistics about a read set
filter out contaminating mate-pair data in a BAM file
find clusters of reads belonging to the same connected component in an assembly graph
extract all kmers from a BWT file


Report bugs to

September 2022 sga 0.10.15