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Cleanup ONT README

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This commit is contained in:
Thomas A. Christensen II 2021-04-13 13:17:45 -06:00
parent 352604237e
commit 54b8fddca8
Signed by: millironx
GPG key ID: 139C07724802BC5D
2 changed files with 6 additions and 3 deletions
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3
.vscode/settings.json vendored
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@ -1,7 +1,10 @@
{ {
"cSpell.words": [ "cSpell.words": [
"Nanopore",
"chmod", "chmod",
"cygpath", "cygpath",
"demux",
"mkdir",
"wphl" "wphl"
] ]
} }

6
ont/README.md
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@ -8,7 +8,7 @@ Note that at the time of writing, the GridION runs Ubuntu 16.04 LTS, and mounts
### `ont-demux` ### `ont-demux`
```bash ```bash
$ ont-demux FAP_FOLDER ont-demux FAP_FOLDER
``` ```
Consolidates all FAST5s into a single gzipped FASTQ using ONT's `guppy_barcoder`. Note that this is for MinKNOW's default settings of 4000 reads/file. It is _highly_ recommended to set the "Number of Reads per File" entry in MinKNOW to 0, and checking "Compress FASTQs" to produce nearly the same results. Consolidates all FAST5s into a single gzipped FASTQ using ONT's `guppy_barcoder`. Note that this is for MinKNOW's default settings of 4000 reads/file. It is _highly_ recommended to set the "Number of Reads per File" entry in MinKNOW to 0, and checking "Compress FASTQs" to produce nearly the same results.
@ -16,7 +16,7 @@ Consolidates all FAST5s into a single gzipped FASTQ using ONT's `guppy_barcoder`
### `ont-transfer` ### `ont-transfer`
```bash ```bash
$ ont-transfer [-s 1|6|12] FAP_FOLDER ont-transfer [-s 1|6|12] FAP_FOLDER
``` ```
Transfers all of the passing FAST5 and FASTQ files to the first available USB drive, skipping empty barcodes based on the number of the first skip passed through the `-s` parameter, consolidating all files of the same type into one folder for easier sorting and uploading. Transfers all of the passing FAST5 and FASTQ files to the first available USB drive, skipping empty barcodes based on the number of the first skip passed through the `-s` parameter, consolidating all files of the same type into one folder for easier sorting and uploading.
@ -32,7 +32,7 @@ Transfers all of the passing FAST5 and FASTQ files to the first available USB dr
See ONT for guppy installation instructions. Others may be installed by opening a terminal and running See ONT for guppy installation instructions. Others may be installed by opening a terminal and running
```bash ```bash
$ sudo apt-get install git parallel -y sudo apt-get install git parallel -y
``` ```
### Instructions ### Instructions