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The result of the assembly is the set of contigs. What else you're looking for? |
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Thanks Anton! How can I tell how large the de novo genome is?
Best,
Kim
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Kim Dorval, PhD
Staff Clinical FAS
647.622.8897
…________________________________
From: Anton Korobeynikov ***@***.***>
Sent: Friday, July 30, 2021 5:49:56 PM
To: ablab/spades ***@***.***>
Cc: Dorval, Kim ***@***.***>; Author ***@***.***>
Subject: Re: [ablab/spades] Using the Illumina BaseSpace Sequence Hub SPAdes Genome Assembler v3.9.0 (#819)
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The result of the assembly is the set of contigs. What else you're looking for?
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There is no need for this. SPAdes does not require such information anywhere. |
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I’m looking for Spades to tell me the size in bp of the de novo genome it assembled. I’m not looking to input a genome size into Spades. How do people understand the size of the assembled de novo genome? The contig file has rows and rows of sequence separated by breaks, shouldn’t the software provide the combined total length of these sequence rows?
Best,
Kim
Kim (Fazil) Dorval, PhD
647.622.8897
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From: Anton Korobeynikov ***@***.***>
Sent: Sunday, September 5, 2021 6:21 PM
To: ablab/spades ***@***.***>
Cc: Dorval, Kim ***@***.***>; Author ***@***.***>
Subject: Re: [ablab/spades] Using the Illumina BaseSpace Sequence Hub SPAdes Genome Assembler v3.9.0 (#819)
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There is no need for this. SPAdes does not require such information anywhere.
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There are many tools that can show this for you. E.g. QUAST. Note that the length of the assembly != the length of the genome |
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I have MiSeq data from a 2x301 from bacterial shot-gun libraries that I ran through the Spades Genome Assembler app in Illumina BaseSpace. I'm looking for a single contig/scaffold FASTA as the output from the SPADES app but only obtained a contigs.fasta and scaffolds.fasta files which have contig sequences (ie. not continuous sequence). Can anyone help me with this?
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