Set a new README

README.md

@@ -1,53 +1,7 @@
+# Fast5Genome
+## [Fast5pipeline](https://raw.githubusercontent.com/AlbertRockG/fast5toGenome/main/fast5pipeline/README.md)
+## [Fastqpipeline](https://raw.githubusercontent.com/AlbertRockG/fast5toGenome/main/fastqpipeline/README.md)
 
-# Fast5pipeline : Bacterial Isolate Genome Sequencing Data Processing pipeline
-
-fast5pipeline is designed to process bacterial isolate whole genome sequencing data obtained using Nanopore sequencing technology (ONT). The pipeline takes fast5 files as input and includes basecalling, demultiplexing, assembling, and polishing of the genome sequences. This pipeline has been design and tested on ubuntu 22.04. You may face some issues while trying to run it in other linux distributions.
-
-```
-OPTIONS:
-
--c: Path to the Guppy configuration file.
--i: Path to the directory containing the raw nanopore sequencing data (fast5 files)
--o: Path to the directory where processed data will be stored. This directory will be created if it doesn't exist.
--k: Barcode kits to be used for barcoding.
--m: medaka model for consensus polishing.
--b: GPU memory control for medaka (optional).
--v: Enable verbosity (optional).
-```
-
-## Instructions to running fast5pipeline 
-### Setup environment
-Before using this pipeline, you need to setup the required environment by installing the following software, if they are not already installed:
-
-- [Guppy Basecalling Software](https://community.nanoporetech.com/docs/prepare/library_prep_protocols/Guppy-protocol/v/gpb_2003_v1_revax_14dec2018/linux-guppy), (C) Oxford Nanopore Technologies plc. Version 6.5.7+ca6d6af, minimap2 version 2.24-r1122 or above
-- [GNU gzip](https://www.gnu.org/software/gzip/)
-- [flye 2.9.2-b1786](https://github.com/fenderglass/Flye) or above
-- [conda](https://conda.io/projects/conda/en/latest/user-guide/install/index.html) or [mamba](https://mamba.readthedocs.io/en/latest/mamba-installation.html#mamba-install)
-- [medaka 1.8.0 or above](https://anaconda.org/bioconda/medaka) (To be installed with conda or mamba in an environment named medaka)
-
-### Run fast5pipeline
-
-To run this pipeline, kindly follow this instructions in your terminal from your home directory:
-
-```bash
-# To get the pipeline source code on your laptop
-git clone https://github.com/AlbertRockG/fast5toGenome
-
-# To add fast5pipeline to the PATH if using bash shell
-echo "export PATH=$PATH:$HOME/fast5Genome" >> .bashrc
-source .bashrc
-
-# To activate the medaka environment, if using conda
-conda activate medaka
-
-# Example of running
-./fast5pipeline -c dna_r9.4.1_450bps_hac.cfg \\
-                -i data/IN_DIR \\
-                -o data/OUT_DIR \\
-                -k SQK-RBK110-96 \\
-                -m r941_min_hac_g507 \\
-                -v
-```
 
 ## Acknowledgments
 
@@ -80,3 +34,4 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
+