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Quast (version 5.2.0+galaxy1)

Assembly mode?:

Useful to know if contigs have been generated all samples together (co-assembly) or on each sample individually (individual assembly)

Use customized names for the input files?:

They will be used in reports, plots and logs

Contigs/scaffolds file:

Reads options:

Currently, the supported read types are Illumina unpaired, paired-end and mate-pair reads, PacBio SMRT, and Oxford Nanopore long reads.

Type of assembly:

Use a reference genome?:

Many metrics can't be evaluated without a reference. If this is omitted, QUAST will only report the metrics that can be evaluated without a reference.

Estimated reference genome size (in bp) for computing NGx statistics:

Type of organism:

Minimum IDY% considered as proper alignment:

Alignments with IDY% worse than this value will be filtered. Note that all alignments with IDY% less than 80.0% will be filtered regardless of this threshold.

Lower threshold for a contig length (in bp):

Shorter contigs won't be taken into account

Are assemblies scaffolds rather than contigs?:

QUAST will add split versions of assemblies to the comparison. Assemblies are split by continuous fragments of N's of length >= 10. If broken version is equal to the original assembly (i.e. nothing was split) it is not included in the comparison.

Is genome large (> 100 Mbp)?:

Use optimal parameters for evaluation of large genomes. Affects speed and accuracy. In particular, imposes --eukaryote --min-contig 3000 --min-alignment 500 --extensive-mis-size 7000 (can be overridden manually with the corresponding options). In addition, this mode tries to identify misassemblies caused by transposable elements and exclude them from the number of misassemblies.

Genes

Genes 0

Alignments

Alignments 0

Advanced options

Advanced options 0

Output files:

What it does

QUAST = QUality ASsessment Tool. The tool evaluates genome assemblies by computing various metrics.

If you have one or multiple genome assemblies, you can assess their quality with Quast. It works with or without reference genome. If you are new to Quast, start by reading its manual page.

Using Quast without reference

Without reference Quast can calculate a number of assembly related-metrics but cannot provide any information about potential misassemblies, inversions, translocations, etc. Suppose you have three assemblies produced by Unicycler corresponding to three different antibiotic treatments car, pit, and cef (these stand for carbenicillin, piperacillin, and cefsulodin, respectively). Evaluating them without reference will produce the following Quast outputs:

Quast report in HTML format

Contig viewer (an HTML file)

Quast report in Tab-delimited format

Quast log (a file technical information about Quast tool execution)

The tab delimited Quast report will contain the following information:

Assembly                  pit_fna cef_fna car_fna
# contigs (>= 0 bp)           100      91      94
# contigs (>= 1000 bp)         62      58      61
Total length (>= 0 bp)    6480635 6481216 6480271
Total length (>= 1000 bp) 6466917 6468946 6467103
# contigs                      71      66      70
Largest contig             848753  848766  662053
Total length              6473173 6474698 6473810
GC (%)                      66.33   66.33   66.33
N50                        270269  289027  254671
N75                        136321  136321  146521
L50                             7       7       8
L75                            15      15      16
# N's per 100 kbp            0.00    0.00    0.00

where values are defined as specified in Quast manual

Quast report in HTML format contains graphs in addition to the above metrics, while Contig viewer draws contigs ordered from longest to shortest. This ordering is suitable for comparing only largest contigs or number of contigs longer than a specific threshold. The viewer shows N50 and N75 with color and textual indication. If the reference genome is available or at least approximate genome length is known (see --est-ref-size), NG50 and NG75 are also shown. You can also tone down contigs shorter than a specified threshold using Icarus control panel:

/repository/static/images/e9991920be0ab8c4/contig_view_noR.png

Also see Plot description section of the manual.

Using Quast with reference

Car, pit, and cef are in fact assemblies of Pseudomonas aeruginosa UCBPP-PA14, so we can use its genome as a reference (by supplying a Fasta file containing P. aeruginosa pa14 genome to Reference genome input box). The following outputs will be produced (note the alignment viewer):

Quast report in HTML format

Contig viewer (an HTML file)

Alignment viewer (an HTML file)

Quast report in Tab-delimited format

Summary of misassemblies

Summary of unaligned contigs

Quast log (a file technical information about Quast tool execution)

With the reference Quast produces a much more comprehensive set of results:

Assembly                  pit_fna cef_fna car_fna
# contigs (>= 0 bp)           100      91      94
# contigs (>= 1000 bp)         62      58      61
Total length (>= 0 bp)    6480635 6481216 6480271
Total length (>= 1000 bp) 6466917 6468946 6467103
# contigs                      71      66      70
Largest contig             848753  848766  662053
Total length              6473173 6474698 6473810
Reference length          6537648 6537648 6537648
GC (%)                      66.33   66.33   66.33
Reference GC (%)            66.29   66.29   66.29
N50                        270269  289027  254671
NG50                       270269  289027  254671
N75                        136321  136321  146521
NG75                       136321  136321  136321
L50                             7       7       8
LG50                            7       7       8
L75                            15      15      16
LG75                           15      15      17
# misassemblies                 0       0       0
# misassembled contigs          0       0       0
Misassembled contigs length     0       0       0
# local misassemblies           1       1       2
# unaligned mis. contigs        0       0       0
# unaligned contigs         0 + 0   0 + 0   0 + 0
                             part    part    part
Unaligned length                0       0       0
Genome fraction (%)        99.015  99.038  99.025
Duplication ratio           1.000   1.000   1.000
# N's per 100 kbp            0.00    0.00    0.00
# mismatches per 100 kbp     3.82    3.63    3.49
# indels per 100 kbp         1.19    1.13    1.13
Largest alignment          848753  848766  662053
Total aligned length      6473163 6474660 6473792
NA50                       270269  289027  254671
NGA50                      270269  289027  254671
NA75                       136321  136321  146521
NGA75                      136321  136321  136321
LA50                            7       7       8
LGA50                           7       7       8
LA75                           15      15      16
LGA75                          15      15      17

where, again, values are defined as specified in Quast manual. You can see that this report includes a variety of data that can only be computer against a reference assembly.

Using reference also produces an Alignment viewer:

/repository/static/images/e9991920be0ab8c4/Align_view.png

Alignment viewer highlights regions of interest as, in this case, missassemblies that can potentially point to genome rearrangements (see more here).