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lbcb-sci / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
MIT License
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Unequal lengths in sequence #66

Open bioramg opened 2 years ago

bioramg commented 2 years ago

I am trying to polish ONT contigs with Illumina reads. But getting an error while using the Illumina pair-end reads.

bwa mem -t 40 -x ont2d ./ont_assembly.fasta /home/Ill_paired.fastq >ont_mapping.sam

racon -m 8 -x -6 -g -8 -w 500 -t 14 /home/Ill_paired.fastq ./ont_mapping.sam ./ont_assembly.fasta > ./ont_polish_racon.fasta

[racon::Overlap::transmute] error: unequal lengths in sequence and overlap file for sequence ST-E00181:968:HGM7HCCX2:1:1101:20496:2610!

I am looking forward to hearing from you.

rvaser commented 2 years ago

Hello, your Illumina pairs probably have the same name which is not supported in the current implementation. Please use this script to modify them before aligning and polishing.

Best regards, Robert

bioramg commented 2 years ago

Thank you for your prompt response.

I am basic to use scripts and all. Is there any other option to modify using the basic commands?

Thank you.

rvaser commented 2 years ago

You can just run it with python racon_preprocess.py Ill_paired.fastq > Ill_paired.preproc.fastq.