How to assemble the bacterial genome; spades
I'm a new user and have no background of computer and genome stuff. I try to assembly the genome. This is what I try to run. I have no idea what I'm doing wrong.
Apples-MacBook-Pro:bin apple$ ./spades.py -k 21,33,55,77 --careful --only-assembler -1-1 11-0910_S7_L001_R1_001.fastq.gz -1-2 11-0910_S7_L001_R2_001.fastq.gz\ -o 11_0911
== Error == Please specify option (e.g. -1, -2, -s, etc) for the following paths: --only-assembler, 11-0910_S7_L001_R1_001.fastq.gz, 11-0910_S7_L001_R2_001.fastq.gz -o, 11_0911
In case you have troubles running SPAdes, you can write to spades.support@bioinf.spbau.ru Please provide us with params.txt and spades.log files from the output directory
Thanks
1 answer
This is not a tutorial, just a regular question. Try:
./spades.py -k 21,33,55,77 --careful --only-assembler -1 11-0910_S7_L001_R1_001.fastq.gz -2 11-0910_S7_L001_R2_001.fastq.gz -o 11_0911
• 0 views
•
link
updated
by
Ram
•
written
by
Adrian Pelin
•
written
by
Adrian Pelin
Log in to answer this question.
More posts like this
-
How to decide Kmer in Spades?
written by bioinfo223 •
-
Spades is running over a week
written by Princy •
-
SAPdes not support single-end data?
written by zhangdengwei
-
solution for SPades to assemble genome with low quality data
written by StudentBio •
-
SPAdes assembler-Error code 255
written by Menia_gavr •
-
Doubt about specifying options in SPAdes
written by inaciogmedeiros •
-
Difficulty using SPAdes - Error relating to access and specificity
written by gfrsims •
-
rnaSPADES, assembly problems
written by leonardomajul •
-
Denovo assembly of Putative Plasmid
written by jigarnt •
-
spades; Failed to align paired reads
written by dogdif •
Sorry about the topic. I try to run according to your suggestion but it's still the same.
Ah I didn't notice you have a typo. Try --only-assembler instead of —only-assembler. I modified my answer to have the corrected version.