sga - String Graph Assembler: de novo genome assembler that uses
string graphs
Program: sga Version: 0.10.15 Contact: Jared Simpson
[js18@sanger.ac.uk]
- 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
- 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
Report bugs to js18@sanger.ac.uk