Why Genome coverage is missing for some assemblies?

Question

[sharmatina189059]

Dear all Can anybody tell me why genome coverage is missing at NCBI for some sample Ids i.e. SAMN04450969 SAMN04450970 SAMN04446560

Answer 1

[andres.firrincieli]

Because the assemblies are missing

[sharmatina189059]

But in PATRIC database, they have mentioned number of contigs.

[andres.firrincieli]

Well, the authors never uploaded the genomes in the NCBI Assemly database.

If you need the coverage, you can calculate that by downloading the fastq files from SRA and the contigs fasta files from PATRIC.

[sharmatina189059]

Thank you so much for your answer. Please tell me one more thing, Do you know how PATRIC has data for contigs. Does PATRIC use its own algorithm for genome assembly?

[andres.firrincieli]

Within PATRIC you can use different assembly pipelines

[sharmatina189059]

Thank you so much for clearing my doubts.