Importing 454 data to run dada2 denoise-pyro


I would like to analyse 454 data using QIIME 2, particularly would like to use the denoise-pyro method of DADA2.

I have experience working with MiSeq data but I am still struggling to get going with 454 data that I was given. I have a single .fna and respective .qual file from the sequencing run, and I was wondering if I can get some help about how to import these to QIIME2, in a format that I can use DADA2.


Hi @Mdavrandi,
QIIME 2 does not have any methods to handle separate fasta and qual files. You will need to convert to fastq with another program, e.g., this QIIME 1 script.

Good luck!

Thanks @Nicholas_Bokulich. Thats exactly where I got stuck, though I finally managed to work it out by doing the following:
Demultiplexed data in QIIME 1;
-m region1_map.txt
-f 454/1.TCA.454Reads.fna
-q 454/1.TCA.454Reads.qual
-b 10
-L 500
-l 380
-d --record_qual_scores
-n 1000000
-o region1_w_Q_split_library

Merged resulting .fna and .qual files by
-f 454/region1_w_Q_split_library/seqs.fna
-q 454/region1_w_Q_split_library/seqs_filtered.qual
-o region1_fastq

Created a fastq file for each sample
-i 454/region1_fastq/seqs.fastq --file_type fastq
-o region1_fastq_files

Compressed the fastq files to fastq.gz using gzip

gzip -r *

Finally imported to QIIME2 using “Fastq manifest” format

qiime tools import --type SampleData[SequencesWithQuality] --input-path se-33-manifest --output-path region1-demux.qza --input-format SingleEndFastqManifestPhred33

I was able to run DADA2 denoise-pyro after going through this. I am not sure if this is ideal or not but it worked. I appreciate if you could point out if there is a better way of doing this.


Looks fine to me. Good luck!

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.