Nextflow Modules
Showing module(s) with keyword "NCBI"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/custom/sratoolsncbisettings | Process | NCBI settings sra-tools prefetch fasterq-dump | Test for the presence of suitable NCBI settings or create them on the fly. |
| nf-core/fastq_download_prefetch_fasterqdump_sratools | Workflow | SRA NCBI sequencing fastq prefetch fasterq-dump | Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA). |
| nf-core/fcs/fcsadaptor | Process | assembly genomics quality control contamination NCBI | Run NCBI's FCS adaptor on assembled genomes |
| nf-core/fcs/fcsgx | Process | assembly genomics quality control contamination NCBI | Run FCS-GX on assembled genomes. The contigs of the assembly are searched against a reference database excluding the given taxid. |
| nf-core/mitohifi/findmitoreference | Process | mitochondrial genome reference genome NCBI | Download a mitochondrial genome to be used as reference for MitoHiFi. NOTE: An optional NCBI API key can be supplied to MITOHIFI_FINDMITOREFERENCE. This should be set using Nextflow's secrets functionality: `nextflow secrets set NCBI_API_KEY <key>` See https://www.nextflow.io/docs/latest/secrets.html for more information. |
| nf-core/ncbitools/vecscreen | Process | assembly genomics quality control contamination vector NCBI | NCBI tool for detecting vector contamination in nucleic acid sequences. This tool is older than NCBI's FCS-adaptor, which is for the same purpose |