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$sga --help Program: sga Version: 0.10.13 Contact: Jared Simpson [js18@sanger.ac.uk] Usage: sga <command> [options] 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 Report bugs to js18@sanger.ac.uk
