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To see the full list, use --help sAdvanced options: sm-s --scaffolds Assemblies are scaffolds, split them and add contigs to the comparison s|-l --labels "label, label, ..." Names of assemblies to use in reports, comma-separated. If contain spaces, use quotes s\-L Take assembly names from their parent directory names s;-e --eukaryote Genome is eukaryotic sG-f --gene-finding Predict genes using MetaGeneMark sˆ-f --gene-finding Predict genes using GeneMarkS (prokaryotes, default) or GeneMark-ES (eukaryotes, use --eukaryote) st --glimmer Use GlimmerHMM for gene prediction (instead of the default finder, see above) sv --mgm Use MetaGeneMark for gene prediction (instead of the default finder, see above) s| --gene-thresholds Comma-separated list of threshold lengths of genes to search with Gene Finding module s4 [default: %s] so --est-ref-size Estimated reference size (for computing NGx metrics without a reference) sƒ --max-ref-number Maximum number of references (per each assembly) to download after looking in SILVA database sZ Set 0 for not looking in SILVA at all [default: %s] s… --blast-db Custom BLAST database (.nsq file). By default, MetaQUAST searches references in SILVA database sŽ --use-input-ref-order Use provided order of references in MetaQUAST summary plots (default order: by the best average value). sP --gage Use GAGE (results are in gage_report.txt) se --contig-thresholds Comma-separated list of contig length thresholds [default: %s] sg-u --use-all-alignments Compute genome fraction, # genes, # operons in QUAST v1.* style. sk By default, QUAST filters Nucmer's alignments to keep only best ones se-i --min-alignment Nucmer's parameter: the minimum alignment length [default: %s] sw --min-identity Nucmer's parameter: the minimum alignment identity (80.0, 100.0) [default: %.1f] sd-a --ambiguity-usage Use none, one, or all alignments of a contig when all of them sd are almost equally good (see --ambiguity-score) [default: %s] s‚ --ambiguity-score Score S for defining equally good alignments of a single contig. All alignments are sorted s by decreasing LEN * IDY% value. All alignments with LEN * IDY% < S * best(LEN * IDY%) are sa discarded. S should be between 0.8 and 1.0 [default: %.2f] sd --unique-mapping Disable --ambiguity-usage=all for the combined reference run, sk i.e. use user-specified or default ('%s') value of --ambiguity-usage sg --strict-NA Break contigs in any misassembly event when compute NAx and NGAx sx By default, QUAST breaks contigs only by extensive misassemblies (not local ones) sy-x --extensive-mis-size Lower threshold for extensive misassembly size. All relocations with inconsistency st less than extensive-mis-size are counted as local misassemblies [default: %s] su --scaffold-gap-max-size Max allowed scaffold gap length difference. All relocations with inconsistency sz less than scaffold-gap-size are counted as scaffold gap misassemblies [default: %s] sy --unaligned-part-size Lower threshold for detecting partially unaligned contigs. Such contig should have se at least one unaligned fragment >= the threshold [default: %s] sx --fragmented Reference genome may be fragmented into small pieces (e.g. scaffolded reference) sy --fragmented-max-indent Mark translocation as fake if both alignments are located no further than N bases s] from the ends of the reference fragments [default: %s] sD Requires --fragmented option. sS --plots-format Save plots in specified format [default: %s] s< Supported formats: %s s, st --memory-efficient Run Nucmer using one thread, separately per each assembly and each chromosome sh This may significantly reduce memory consumption on large genomes s --space-efficient Create only reports and plots files. .stdout, .stderr, .coords and other aux files will not be created sŽ This may significantly reduce space consumption on large genomes. Icarus viewers also will not be built s`-1 --reads1 File with forward reads (in FASTQ format, may be gzipped) s`-2 --reads2 File with reverse reads (in FASTQ format, may be gzipped) s9 --sam SAM alignment file s9 --bam BAM alignment file sn Reads (or SAM/BAM file) are used for structural variation detection and sL coverage histogram building in Icarus sX --sv-bedpe File with structural variations (in BEDPE format) sSpeedup options: st --no-check Do not check and correct input fasta files. Use at your own risk (see manual) s8 --no-plots Do not draw plots sS --no-html Do not build html reports and Icarus viewers sB --no-icarus Do not build Icarus viewers sx --no-snps Do not report SNPs (may significantly reduce memory consumption on large genomes) sM --no-gc Do not compute GC% and GC-distribution sy --no-sv Do not run structural variation detection (make sense only if reads are specified) sI --no-gzip Do not compress large output files s] --fast A combination of all speedup options except --no-check sHidden options: s0-d --debug Run in a debug mode sI--no-portable-html Do not embed CSS and JS files in HTML report si-c --min-cluster Nucmer's parameter: the minimum length of a cluster of matches [default: %s] sD-j --save-json Save the output also in the JSON format sF-J --save-json-to Save the JSON output to a particular path s‹--read-support Use read coverage specified in contig names (SPAdes/Velvet style) for calculating Avg contig read support sW--cov File with read 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