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           rmdup           duplicate read removal - superceded by sga filter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