Decided to compare the Redundans using Canu as reference and Redundans using Racon as reference. Both reference assemblies were just our PacBio data.

Jupyter notebook (GitHub): 20171005_docker_oly_redundans.ipynb

Notebook is also embedded at the end of this post.

• Redundans/Canu assembly (scaffolded assembly; FASTA): http://owl.fish.washington.edu/Athaliana/20171004_redundans/scaffolds.reduced.fa

• Racon PacBio assembly (contigs: FASTA): http://owl.fish.washington.edu/Athaliana/201709_oly_pacbio_assembly_minimap_asm_racon/20170918_oly_pacbio_racon1_consensus.fasta

Results:

• Redundans/Racon Output folder: http://owl.fish.washington.edu/Athaliana/20171005_redundans/

• Redundans/Racon assembly (scaffolded assembly; FASTA): http://owl.fish.washington.edu/Athaliana/20171005_redundans/scaffolds.reduced.fa

• QUAST output folder (default settings): http://owl.fish.washington.edu/Athaliana/quast_results/results_2017_10_06_22_21_06/

• QUAST output folder (–scaffolds setting): http://owl.fish.washington.edu/Athaliana/quast_results/results_2017_10_06_22_27_26/

It should be noted that the paired reads for each of the BGI mate-pair Illumina data did not assemble, just like last time I used them:

• 160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_2.fq.gz
• 160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_2.fq.gz
• 160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_2.fq.gz
• 160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_2.fq.gz
• 160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.gz
• 160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_2.fq.gz

Redundans with Canu is better, suggesting that the Canu assembly is the better of the two PacBio assemblies (which we had already suspected).

QUAST comparison using default settings:

Interactive link:http://owl.fish.washington.edu/Athaliana/quast_results/results_2017_10_06_22_21_06/report.html

QUAST comparison using –scaffolds setting:

Interactive link: http://owl.fish.washington.edu/Athaliana/quast_results/results_2017_10_06_22_27_26/report.html