NAME¶

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

SYNOPSIS¶

sga <command> [options]

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

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

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

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

Report bugs to js18@sanger.ac.uk

September 2022

sga 0.10.15