sga1

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