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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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using hybridSPAdes in plasmid mode #20

Open nenadmacesic opened 7 years ago

nenadmacesic commented 7 years ago

Hi, I am trying to assemble a plasmid using paired-end Illumina reads from a whole genome sequence with Oxford Nanopore long reads from a plasmid DNA extraction from the same organism.

The command that I used was:

spades.py --careful --plasmid --pe1-1 NR3055_1.fastq.gz --pe1-2 NR3055_2.fastq.gz \
--nanopore NR3055_nano_ltd.fastq -o pNR3055_ltd

SPAdes reads the libraries correctly but then does not seem to incorporate the long reads - I have attached the log. Any advice is much appreciated!

spades_log.docx

asl commented 7 years ago

Hello

Thank you for your interest in SPAdes.

Why do you think SPAdes did not use the long reads?

On May 19, 2017 06:49, "nenadmacesic" notifications@github.com wrote:

Hi, I am trying to assemble a plasmid using paired-end Illumina reads from a whole genome sequence with Oxford Nanopore long reads from a plasmid DNA extraction from the same organism.

The command that I used was:

spades.py --careful --plasmid --pe1-1 NR3055_1.fastq.gz --pe1-2 NR3055_2.fastq.gz \ --nanopore NR3055_nano_ltd.fastq -o pNR3055_ltd

SPAdes reads the libraries correctly but then does not seem to incorporate the long reads - I have attached the log. Any advice is much appreciated!

spades_log.docx https://github.com/ablab/spades/files/1014265/spades_log.docx

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nenadmacesic commented 7 years ago

Thank you for the reply.

When I look in the log file there are the following lines: 'Closing gaps with long reads' 'Closed 0 gaps'.

When I compare the resulting graph with a graph that I obtained using the Illumina sequences alone, it is almost identical (~140 nodes and ~190 edges). This occurred regardless of using different cutoffs to select out the Nanopore reads prior to assembly (eg. >1K, >2K etc.).

asl commented 7 years ago

'Closed 0 gaps'.

It's ok. These gaps are the coverage gaps in Illumina data, it's not ancient "gaps due to repeat masking" thing that was common 10 years ago.

When I compare the resulting graph with a graph that I obtained using the Illumina sequences alone, it is almost identical (~140 nodes and ~190 edges).

Have you looked into plasmid components? Have you reviewed them on repeat contents?