Program: sga Version: 0.9.17 Contact: Jared Simpson [js18@sanger.ac.uk] Usage: sga[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 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 bwt2fa transform a bwt back into a set of sequences convert-beetl convert an index file constructed with BEETL into SGA's format Experimental commands: graph-diff find and report strings that differ between two graphs gen-ssa generate a sampled suffix array for the given set of reads correct-long correct long reads stats print useful statistics about the read set connect resolve the complete sequence of a paired-end fragment scaffold generate ordered sets of contigs using distance estimates scaffold2fasta convert the output of the scaffold subprogram into a fasta file filterBAM filter out contaminating mate-pair data in a BAM file cluster find clusters of reads belonging to the same connected component var2vcf convert aligned variant sequences found by graph-diff into a VCF file hapgen generate candidate haplotypes from an assembly graph gapfill fill intra-scaffold gaps metagenome assemble contigs from metagenomics data Deprecated commands: rmdup duplicate read removal - superceded by sga filter Report bugs to js18@sanger.ac.uk