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This article is to share with you about the usefulness of QUAST. The editor thinks it is very practical, so share it with you as a reference and follow the editor to have a look.

For different kmer or different software genome assembly results, we usually use N50 and other indicators to evaluate.

For an assembled sequence, whether contig or scaffold, first sort each sequence according to its length from large to small, and then accumulate the length from the first sequence until the accumulated length exceeds 50% of the total length. In this case, the length of the last accumulated contig is the length of N50. The schematic diagram is as follows

In the picture above, the length of N50 is 60, which is similar to the concept of N50, and there are N75, N90 and so on. These indicators can be collectively referred to as Nx. The larger the Nx, the longer the length of the assembled fragment, which confirmed that the better the assembly result.

In addition to Nx indicators, there are also Lx indicators, such as L50, which refers to the cumulative number of contig, as shown below

The value of L50 in the above figure is 3. In the actual analysis, we can use the existing software to calculate N50, L50 and other indicators, quast is one of the most commonly used software. The software has an online service and the link is as follows

Http://quast.bioinf.spbau.ru/

Just upload the contig or scaffold sequence in fasta format and submit it. Although the online service is convenient, it is also limited. The size of the uploaded fasta file cannot exceed 100Mb. For the actual genome project, it can not meet the requirements. At this point, you can download the software to the local server and run it.

The installation process is as follows

Wget https://sourceforge.net/projects/quast/files/quast-4.6.3.tar.gztar xzvf quast-4.6.3.tar.gzcd quast-4.6.3/

Quast is based on python development, since the matplotlib library to draw, to ensure that python and matplotlib are installed, and then directly download the source code, decompression can be used.

The usage is as follows

Python quast.py-t 10-o test1_out contigs.fasta

The-t parameter specifies the number of threads, and the-o parameter specifies the directory where the results are output. After the run is complete, the output directory generates the following files

├── basic_stats ├── icarus.html ├── icarus_viewers ├── quast.log ├── report.html ├── report.tex ├── report.tsv ├── report.txt ├── transposed_report.tex ├── transposed_report.tsv └── transposed_report.txt

Just look at the report.html file directly.

1. Contig basic information statistical table

Quast will count the number of contig of different lengths, as well as indicators such as N50 and L50. The example results are as follows

2. Nx length distribution curve

The Abscissa is Nx, and the ordinate is the value of Nx. The diagram is as follows

3. Cumulative curve of contig length

Abscissa is the number of contig, ordinate is the cumulative length, the schematic diagram is as follows

4. GC content distribution map

According to the GC content distribution map of the window, quast divides each contig into windows of length 100bp, and calculates the GC content of each window. The Abscissa is the GC content and the ordinate is the number of windows. The diagram is as follows.

Contig GC content distribution map, for each contig, statistics GC content, Abscissa is GC content, ordinate is contig number, schematic diagram is as follows

Thank you for reading! This is the end of this article on "what's the use of QUAST?". I hope the above content can be of some help to you, so that you can learn more knowledge. if you think the article is good, you can share it for more people to see!

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