Basic Statistics

Summary

The module collects basic information for the sequencing reads and evaluate the reference assemblies using QUAST, a genome assembly evaluation tool.


Sequencing reads

Sequencing reads information


Assembly evaluation

QUAST command:

python3 SQUAT/quast/quast.py <assembly> -o <output_dir> --min-contig 200 -t <num_threads> -s

Assembly evaluation


Assembly evaluation (GAGE mode)

Note that if GAGE mode is activated in QUAST, statistics such as NX and LX will be replaced by NGX and LGX in the table.

QUAST command:

python3 SQUAT/quast/quast.py <assembly> -o <output_dir> --min-contig 200 -t <num_threads> -s -R <reference genome> --gage

Assembly evaluation GAGE

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