Comments (4)
Error correction is optional and if errors are present in sequences it will affect their ability to map to decontaminant reference sequences. That was my thought anyways. SPAdes will perform an additional step of error correction in its protocol.
from atlas.
For publication, you normally want to upload raw reads. But at least for human metagenomics one should remove the reads from the host for confidentiality reasons. That was a second thought to put the decontamination step first and all the quality filtering and error correction later?
from atlas.
That definitely makes sense in that context.
We now force users to either start with single- or paired-end after de-interleaving their own reads using reformat.sh. It seems like a simple switch and I'm open to it.
from atlas.
The rule order has been updated to reflect corrections highlighted in the original issue.
from atlas.
Related Issues (20)
- Error in rule run_vamb HOT 2
- NaNs in samples.tsv HOT 6
- atlas metatranscriptome data - MissingOutputException in rule run_spades HOT 19
- Error in localrule parse_vamb_output: HOT 5
- atlas downdload fail HOT 6
- Setting eggNOG_use_virtual_disk to true HOT 4
- Error in rule multiqc_mapping_genome due to incontability with python 3.12 HOT 13
- Creating envs (--conda-create-envs-only) is running without error, but not creating envs HOT 1
- atlas init-public no such command HOT 2
- Run atlas genomes without the taxonomy output HOT 2
- Disk_mem not sufficient HOT 6
- Error in rule HOT 5
- Error in rule run_spades HOT 19
- MissingOutputException HOT 2
- Error in rule get_bins: only 1 conting found in samples
- Error during DRAM download; processing vogdb HOT 6
- plans for supporting fungi HOT 5
- What does "max" in the combined_contig_stats.tsv mean? HOT 1
- Support for highly accurate long reads? HOT 1
- Error in rule build_qc_report: ModuleNotFoundError: No module named 'numpy._version' HOT 2
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