NAME

       sga - String Graph Assembler: de novo genome assembler that uses string graphs

SYNOPSIS

       sga <command> [options]

DESCRIPTION

       Program: sga Version: 0.10.15 Contact: Jared Simpson [js18@sanger.ac.uk]

   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

REPORTING BUGS

       Report bugs to js18@sanger.ac.uk