Description of bug
Hi all,
I did cDNA synthesis to amplify both RNA and DNA viruses and I used NexteraXT (Illumina) to amplify the vrial commmunities and and sequencing with NextSeq500 using a 75cycle kit with paired end 40nt reads and 6nt+6nt dual indexing.
I check the sequence data using Kraken and I can see the viral communities as we spiked some of the samples with known viruses and the data makes sense. However, I was also interested into metaviralspades.py. I was able to generate the data but when I blast the contigs/scafold only pseudomonas aeruginosa shows up (which is a bacteria). I was wondering if I can use spades for my sequence data (as it is 40bp).
I attached the log and parameter file.
I upload my scaffold file too.
spades.log
spades.log
params.txt
params.txt
scaffolds.txt
SPAdes version
3.15.4
Operating System
Ubuntu 22.04.2 LTS
Python Version
3.10.11
Method of SPAdes installation
Manual
No errors reported in spades.log
Description of bug
Hi all,
I did cDNA synthesis to amplify both RNA and DNA viruses and I used NexteraXT (Illumina) to amplify the vrial commmunities and and sequencing with NextSeq500 using a 75cycle kit with paired end 40nt reads and 6nt+6nt dual indexing.
I check the sequence data using Kraken and I can see the viral communities as we spiked some of the samples with known viruses and the data makes sense. However, I was also interested into metaviralspades.py. I was able to generate the data but when I blast the contigs/scafold only pseudomonas aeruginosa shows up (which is a bacteria). I was wondering if I can use spades for my sequence data (as it is 40bp).
I attached the log and parameter file.
I upload my scaffold file too.
spades.log
spades.log
params.txt
params.txt
scaffolds.txt
SPAdes version
3.15.4
Operating System
Ubuntu 22.04.2 LTS
Python Version
3.10.11
Method of SPAdes installation
Manual
No errors reported in spades.log