Banana Slug Genomics

  $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