Quast

QUAST is a tool for evaluating the quality of genome or metagenome assemblies. In this module, QUAST assesses assembled scaffold/scaftig FASTA files and summarizes key assembly statistics.

Workflow

Workflow 建议填写内容

1. Input assembly FASTA
   Upload an assembled FASTA file, such as scaffold or scaftig sequences.

2. Run assembly quality assessment
   Use QUAST to evaluate the input assembly with a minimum contig length threshold.

3. Extract key metrics
   Collect assembly statistics including total length, number of contigs, largest contig, N50, N90, L50, and GC content.

4. Generate report files
   Output a summary table and the original QUAST report files for downstream review.

Data

Example dataset include 100 bp illumina WGS reads consist of ~10% subsets of 3 paired end sets of reads from the following publication:
The sample names in the original publication used to generate the toy dataset is ERR260162 (sample1)

Result：

v0.2: The pipeline is stored in Code Repository: CRS1234920585075896320. The computational docker enrionment is stored in Software Repository: SRS1234913519569481728.

Reproducibility

The pipeline utilizes code CRS1234920585075896320 and Docker image SRS1234913519569481728, both of which are stored in the BMAP repositories.

Usage

1. Select the application 'Quast'
2. Click on the 'Analysis' button
3. Click on the 'Metagenomics pipeline'
4. Fill in the request parameters

5. Upload the compressed data in gz or rar format.