atlas

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default maping rate with bbmap is 0.76

3

I realized that the default min mapping id is set to, which corresponds to the default of bbmap but is very low for metagenomic reads mapping. I usually use 0.9....

SilasK

Pooled assembly for mapping of individual metagenomes within a study site

11

Hello! I have a set of metagenomes of samples that were obtained from a subsurface petroleum reservoir. These samples comprise different types (_i.e.,_ formation water, production water, crude oil, and...

dscheah

understanding filter step

3

So, the mock data I used (retrieved from another lab) contain reads with quality set to 'I' corresponding to 40 in phred 33 but 9 in phred 66. In the...

noirot

SilasK

Contig annotation and quantification

5

Hello, If I have assembled contigs and just want to annotation/quantify (eggnog4, SEED etc) is that option still available? Not the bins but the contigs directly. I couldn't find it...

raw937

Exiting because a job execution failed.

2

Hello, I think something went wrong somewhere and it could not finish the job. 2022-08-12 15:10:26 (301 MB/s) - ‘/home/nwezejus/Peat_metagenome2022/ATLAS/databases/adapters.fa’ saved [13954/13954] [Fri Aug 12 15:10:27 2022] Finished job 8....

Justan6

SilasK

Error in rule

1

What does this mean about "QC_se.fastq.gz"?

luozhy88

Can this function be realized for atlas?

4

Hi,Can this function be realized by atlas? Coassembly mode: Reads from all samples are pooled and a single assembly is performed. Then reads from individual samples are mapped to the...

luozhy88

screen samples before starting

SilasK