GenomeRefBased - aechchiki/SIB_LongReadsWorkshop_Zurich18 GitHub Wiki

Reference-based methods

Section: Genome assembly assessment [2/5].

In the ideal case, we have available reference genome we can use to evaluate how correct our assembly is. Very straightforward tool that allows integrated comparison of multiple assemblies to known reference is called quast.

Another option would be to align the assembly to reference using one of the whole genome aligning tools like Mummer, LAST or Minimap2.

Quast

If you have your own assembly, just get this reference, otherwise you can also download assemblies from shared directory.

# backup assembly
# from Canu
wget https://drive.switch.ch/index.php/s/6yhvPsyAQQ52qH8/download -O canu.tar.gz
# from Miniasm
wget https://drive.switch.ch/index.php/s/TiTZjzUgMZzRNYo/download -O miniasm.tar.gz
# from Racon
wget https://drive.switch.ch/index.php/s/uo0c5HQLaMtV32W/download -O racon.fasta.gz
# get the refernece assembly for chr4 (Ensembl)
wget https://drive.switch.ch/index.php/s/po5MjyCAQmwYAG8/download -O dmel_ch4_reference.fasta.gz

You can install the last version from:

wget https://sourceforge.net/projects/quast/files/quast-5.0.1.tar.gz
tar -xzvf quast-5.0.1.tar.gz

Or use the one available on Docker. The executable we need is quast.py.

sudo quast.py -o <output_filename> -R <path_to_ref.fasta> <path_to_canu.fasta> <path_to_miniasm.fasta> <path_to_racon.fasta>

In the output folder, there is a nice overview of differences between genome assemblies.

aechchik@dee-serv03:/scratch/beegfs/monthly/aechchik/dw$ ll -h out_quast/
total 476K
drwxr-xr-x 2 aechchik dee_robi    0 Nov  7 13:20 aligned_stats
drwxr-xr-x 2 aechchik dee_robi    8 Nov  7 13:19 basic_stats
drwxr-xr-x 4 aechchik dee_robi   29 Nov  7 13:20 contigs_reports
drwxr-xr-x 2 aechchik dee_robi    4 Nov  7 13:20 genome_stats
-rw-r--r-- 1 aechchik dee_robi  53K Nov  7 13:20 icarus.html
drwxr-xr-x 2 aechchik dee_robi    2 Nov  7 13:20 icarus_viewers
-rw-r--r-- 1 aechchik dee_robi 6.3K Nov  7 13:20 quast.log
-rw-r--r-- 1 aechchik dee_robi 397K Nov  7 13:20 report.html
-rw-r--r-- 1 aechchik dee_robi 3.0K Nov  7 13:20 report.tex
-rw-r--r-- 1 aechchik dee_robi 1.6K Nov  7 13:20 report.tsv
-rw-r--r-- 1 aechchik dee_robi 3.8K Nov  7 13:20 report.txt
-rw-r--r-- 1 aechchik dee_robi 2.4K Nov  7 13:20 transposed_report.tex
-rw-r--r-- 1 aechchik dee_robi 1.6K Nov  7 13:20 transposed_report.tsv
-rw-r--r-- 1 aechchik dee_robi 3.6K Nov  7 13:20 transposed_report.txt

Backup

In case you need it, we provide backup:

wget https://drive.switch.ch/index.php/s/6Aa8qXIrsbM4N3x/download -O quast.tar.gz

Get the html file and visualize it.

Compare!

quast1

For Canu:

quast2

How does it look like?

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