SGA(1)

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