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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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The number of contigs generated is significantly lower than expected #1252

Open liusihang opened 8 months ago

liusihang commented 8 months ago

Description of bug

Hello, I recently ran metaviralSPAdes on a set of general environmental samples without targeted viral enrichment, and I noticed that the number of contigs generated is significantly lower than expected. I'm reaching out to seek insights or suggestions on why this might be the case and how to potentially improve the outcome.

spades.log

spades.log

params.txt

params.txt

SPAdes version

SPAdes version: 3.15.5

Operating System

Ubuntu 20.02

Python Version

Python version: 3.12.2

Method of SPAdes installation

conda

No errors reported in spades.log

contigs.zip

Update

The metaspades mode was employed to test the same data, utilizing the --only-assembler option. A significantly larger contig fasta file was generated. image params.txt spades.log

asl commented 8 months ago

Hello

How have you estimated the expected number?

liusihang commented 8 months ago

Hello

How have you estimated the expected number?

Hello， I initially utilized MEGAHIT for the assembly of genomic data, yielded a contig FASTA file approximately 1.2GB in size after removing contigs < 1000bp.