A directory for fast5pipeline

AlbertRockG · Jun 4, 2024 · 98d6b23 · 98d6b23
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diff --git a/fast5pipeline/README.md b/fast5pipeline/README.md
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+
+# 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
+
+I would like to express my gratitude to the following individuals and organizations for their valuable contributions and support:
+
+- [Marco](https://github.com/zwets), a senior Bioinformatician, for providing guidance and assistance throughout the process.
+- FAO (Food and Agriculture Organization), SeqAfrica, and FlemingFund for their support in funding and resources.
+- The Noguchi Memorial Institute for Medical Research for providing the infrastructure and facilities for this project.
+
+## License
+
+MIT License
+
+Copyright (c) 2023 Albert Rock A. Gangbadja
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+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.
diff --git a/fast5pipeline → fast5pipeline/fast5pipeline b/fast5pipeline → fast5pipeline/fast5pipeline
@@ -125,18 +125,18 @@ BATCHSIZE=100
 ### ARGS PARSING -----------------------------------------------------------------------------------------------------------------------
 # Parse command-line options
 
-while getopts "c:i:o:k:m:b:v" opt; do
-    case "${opt}" in
-        c) guppy_config=${OPTARG};;
-        i) input_dir=${OPTARG};;
-        o) output_dir=${OPTARG};;
-        k) barcode_kits=${OPTARG};;
-        m) medaka_model=${OPTARG};;
-        b) BATCHSIZE=${OPTARG};;
-        v) VERBOSE=1;;
-        *) usage;;
-    esac
-done
+# while getopts "c:i:o:k:m:b:v" opt; do
+#     case "${opt}" in
+#         c) guppy_config=${OPTARG};;
+#         i) input_dir=${OPTARG};;
+#         o) output_dir=${OPTARG};;
+#         k) barcode_kits=${OPTARG};;
+#         m) medaka_model=${OPTARG};;
+#         b) BATCHSIZE=${OPTARG};;
+#         v) VERBOSE=1;;
+#         *) usage;;
+#     esac
+# done
 
 # Check if all required options are provided