Hello (posting again because i didn't get any anwer on last post)
I have performed some genome assemblies using canu assembler and i am not able to fully understand its output files. I did find a 7/8 year old post (can't find it again) but i personally think that things might have changed since then so I am looking for current experience from you.
Organism: Fungus fusarium Data type: Nanopore ONT
After a successfull genome assembly i got the following files in output directory
- NP01.contigs.fasta
- NP01.contigs.layout.readToTig
- NP01.contigs.layout.tigInfo
- NP01.correctedReads.fasta.gz
- NP01.trimmedReads.fasta.gz
- NP01.unassembled.fasta
Looking around, i know that NP01.contigs.fasta is the main assembly file. I am not sure about the NP01.unassembled.fasta
Question 1: What is this unassembled file about. Should i consider using this file like
- polish the unassembled contigs using Racon+Raw ONT reads
- then merge them into main assembly file ?
Or just ignore this file and use the NP01.contigs.fasta for downstream processing and polishing ?
Question 2: What are the corrected reads? I mean what is a general process which generates corrected reads or how canu corrects teh reads ?
Question 3: What is the use case of readToTig and tigInfo files ?
Please read the documentation: https://canu.readthedocs.io/en/latest/tutorial.html#outputs