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