.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.2. .TH SGA "1" "September 2022" "sga 0.10.15" "User Commands" .SH NAME sga \- String Graph Assembler: de novo genome assembler that uses string graphs .SH SYNOPSIS .B sga \fI\, \/\fR[\fI\,options\/\fR] .SH DESCRIPTION Program: sga Version: 0.10.15 Contact: Jared Simpson [js18@sanger.ac.uk] .SS "Commands:" .TP preprocess filter and quality\-trim reads .TP index build the BWT and FM\-index for a set of reads .TP merge merge multiple BWT/FM\-index files into a single index .TP bwt2fa transform a bwt back into a set of sequences .TP correct correct sequencing errors in a set of reads .TP fm\-merge merge unambiguously overlapped sequences using the FM\-index .TP overlap compute overlaps between reads .TP assemble generate contigs from an assembly graph .TP oview view overlap alignments .TP subgraph extract a subgraph from a graph .TP filter remove reads from a data set .TP rmdup duplicate read removal .TP gen\-ssa generate a sampled suffix array for the given set of reads .TP scaffold generate ordered sets of contigs using distance estimates .TP scaffold2fasta convert the output of the scaffold subprogram into a fasta file .TP gapfill fill intra\-scaffold gaps .SS "Variant Calling Commands:" .TP graph\-diff compare reads to find sequence variants .TP graph\-concordance check called variants for representation in the assembly graph .TP rewrite\-evidence\-bam fill in sequence and quality information for a variant evidence BAM .TP haplotype\-filter filter out low\-quality haplotypes .TP somatic\-variant\-filters filter out low\-quality variants .SS "Experimental commands:" .TP preqc perform pre\-assembly quality checks on a set of reads .TP stats print summary statistics about a read set .TP filterBAM filter out contaminating mate\-pair data in a BAM file .TP cluster find clusters of reads belonging to the same connected component in an assembly graph .TP kmer\-count extract all kmers from a BWT file .SH "REPORTING BUGS" Report bugs to js18@sanger.ac.uk