FastQuast: Fast and simple Quality Assessment Tool for Large Genomes
FastQuast is a tool for assessing the quality of genome assemblies. It is designed to be fast and simple, with usage patterns similar to the popular Quast tool. However, FastQuast has been rewritten from scratch to optimize for speed, providing results up to 5 times faster than Quast.
Features
FastQuast provides the following features:
Works with python 2.7 and 3.6+
Fast and efficient quality assessment of genome assemblies similar to the classic Quast
User-defined thresholds for contig length
Ability to save reports in TSV format (if you want more post-processing friedly format, but I prefer classic Quast txt format)
Installation
FastQuast can be installed via pip or conda. First, make sure you have either pip or conda installed on your system.
Installation via conda
conda install -c bioconda fastquast
Installation via pip
To install FastQuast via pip, run the following command:
pip install fastQuast
Usage
You can use both variant:
fastQuast -h
and
fastquast -h
The simplest way to use:
fastquast you_genome.fasta
And it will create you_genome.quast file in the same place where you_genome.fasta located.
Full usage and options:
fastquast [-h] [-o OUTPUT_DIR] [-s] [-m MIN_CONTIG] [-l LABELS] [--tsv]
files_with_contigs [files_with_contigs ...]
Fast and simple Quality Assessment Tool for Genome Assemblies
positional arguments:
files_with_contigs List of files with contigs
optional arguments:
-h, --help show this help message and exit
-o OUTPUT_DIR, --output-dir OUTPUT_DIR
Directory to store all result files [default: replace file extension with quast
extension]
-s, --split-scaffolds
Split assemblies by continuous fragments of N's and add such "contigs" to the
comparison [default: False]
-m MIN_CONTIG, --min-contig MIN_CONTIG
Lower threshold for contig length [default: 1]
-l LABELS, --labels LABELS
Names of assemblies to use in reports, comma-separated. If contain spaces, use
quotes
--tsv Save report in TSV format to the specified file [default: false]
This will assess the quality of the contigs.fasta assembly, set a minimum contig length of 500 bp, label the assembly as “Assembly A” and “Assembly B” in the report, save the report in both human-readable and TSV format, and store the results in the results/ directory.
FastQuast: Fast and simple Quality Assessment Tool for Large Genomes
FastQuast is a tool for assessing the quality of genome assemblies. It is designed to be fast and simple, with usage patterns similar to the popular Quast tool. However, FastQuast has been rewritten from scratch to optimize for speed, providing results up to 5 times faster than Quast.
Features
FastQuast provides the following features:
Installation
FastQuast can be installed via pip or conda. First, make sure you have either pip or conda installed on your system.
Installation via conda
Installation via pip
To install FastQuast via pip, run the following command:
Usage
You can use both variant:
and
The simplest way to use:
And it will create you_genome.quast file in the same place where you_genome.fasta located.
Full usage and options:
Example
Here’s an example of how to use FastQuast:
This will assess the quality of the contigs.fasta assembly, set a minimum contig length of 500 bp, label the assembly as “Assembly A” and “Assembly B” in the report, save the report in both human-readable and TSV format, and store the results in the results/ directory.