will-rowe
commented
3 years ago Hi @mhelbom14. Thanks for getting in touch. Unfortunately this pipeline is designed to work with amplicon sequencing data, specifically the Network ARTIC schemes, and doesn't perform an assembly.
Maybe something like VGEA would be more suitable?
mhelbom14
Hello,
I used a metagenomic approach to sequence SARS-CoV2 genome and the data were very good with 100% coverage and 422x depth converge. now I want to assemble my reads and get the consensus sequence and the variant file. I want to use the workflow described here but I cant optimize my code to work with my data. I did the basecalling and the demultiplexing for the data and I have the pass fastq files. I want to start from the artic minion command. I tried to run the command with my data but got this error. " (artic-ncov2019) lab123@DESKTOP-2AI9TES:/mnt/d/Mohammad/Nanopore/Analysis/covid-19$ artic minion --normalise 200 --threads 4 --read-file /mnt/c/data/covid-19/covid-19/1/20201102_1452_MN31812_FAL01681_d9c4ed35/fastq_pass/barcode01/FAL01681_pass_barcode01f475dc98*.fastq --fast5-directory /mnt/c/data/covid-19/covid-19/1/20201102_1452_MN31812_FAL01681_d9c4ed35/fast5_pass/barcode01/ --sequencing-summary /mnt/c/data/covid-19/covid-19/1/20201102_1452_MN31812_FAL01681_d9c4ed35/sequencing_summary_FAL01681_f475dc98.txt usage: artic [-h] [-v] {extract,basecaller,demultiplex,minion,gather,guppyplex,filter,rampart,export,run} ... artic: error: unrecognized arguments: /mnt/c/data/covid-19/covid-19/1/20201102_1452_MN31812_FAL01681_d9c4ed35/fastq_pass/barcode01/FAL01681_pass_barcode01_f475dc98_100.fastq /mnt/c/data/covid-19/covid-19/1/20201102_1452_MN31812_FAL01681_d9c4ed35/fastq_pass/barcode01/FAL01681_pass_barcode01_f475dc98_101.fastq 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/mnt/c/data/covid-19/covid-19/1/20201102_1452_MN31812_FAL01681_d9c4ed35/fastq_pass/barcode01/FAL01681_pass_barcode01_f475dc98_99.fastq " how could I fix it? and for the "scheme-directory" I don't have scheme directory because I didn't use artic network primers. I used SISPA A/B method