Work in progress TODO:
- add read count to header
lorem ipsum
- Takes as input MinION fastq files and primer sequence
- Searches for the primer sequence in each read cuts them up, creating a fastq file for each
- Has option for RCA and dumbell/LAMP methods
- For dumbell method, has option to re-orientate reads
- It does not remove the primer sequence, so these must be sof clipped in alignment (or trimmed before)
- Does this cause issue with the consensus calling script? I dont think so (but its easy to edit if it does)
- Has option for RCA and dumbell/LAMP methods
| Flag | Description | Default Value |
|---|---|---|
| -f, --fastq | The full path to the fastq file (not zipped) to process. | Require Input |
| -p, --primer | The sequence of the forward primer used. | Require Input |
| -t, --is_dumbell | Is this a dumbell amplicon, i.e., will it forward and comp in same sequence. | NA |
| -c, --no_dumbell_comp | If this a dumbell amplicon, should the complemtary sequence NOT be complemented? | NA |
| -d, --distance | Maximum Levenshtein distance for primer search | 2 |
| -mx, --min_len | Minimum length of cut sequence | 2 |
| -mn, --max_len | Maximum length of cut sequence | 9999999 |
| -o, --out | Output folder | cwd |
- Takes as input the cut up fastq files for each read and creates a consensus for each
- make sure only taking those with multiple reads, and then adding the singletons at the end if user wants
- Two methods available
- Output is a fastq (or fasta) file with the consensus reads (one for each amplicon) that can be used downstream as usual
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