hifiadapterfilt
Description¶
Convert .bam to .fastq and remove reads with remnant PacBio adapter sequences
Installation¶
ebi-metagenomics/hifiadapterfilt
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install hifiadapterfilt
Tools¶
hifiadapterfilt¶
Convert .bam to .fastq and remove CCS reads with remnant PacBio adapter sequences
Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] |
- |
fastq |
file | Fastq pacbio hifi raw reads file. The tool AUTOMATICALLY detects fastq files from the input folder, hence an explicit call of "fastq" is not needed. | *.fastq |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
filt |
file | - | |
blast_search |
file | - | |
stats |
file | - | |
headers |
file | - | |
versions |
file | - |
