table of contents
SGA(1) | User Commands | 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
September 2022 | sga 0.10.15 |