sga(1) String Graph Assembler: de novo genome assembler that uses string graphs

SYNOPSIS

sga ,<command> /[,options/]

DESCRIPTION

Program: sga Version: 0.10.14 Contact: Jared Simpson [[email protected]]

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 [email protected]