Banana Slug Genomics

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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
Banana Slug Genomics

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