nestlink-pipeline

Pipeline to generate accurate consenus sequences of NestLink libraries.

https://github.com/fabianackle/nestlink-pipeline

Science Score: 54.0%

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Repository

Pipeline to generate accurate consenus sequences of NestLink libraries.

Basic Info

Host: GitHub
Owner: fabianackle
License: mit
Language: Python
Default Branch: main
Homepage:
Size: 119 KB

Statistics

Stars: 0
Watchers: 1
Forks: 0
Open Issues: 0
Releases: 0

Created almost 2 years ago · Last pushed 6 months ago

Metadata Files

Readme License Citation

NestLink-pipeline

NestLink-pipeline is a pipeline for processing barcoded protein variant libraries and NestLink libraries sequenced by nanopore sequencing. Reads are binned according to their barcodes or flycodes (UMIs). Accurate consensus sequences are calculated using Medaka. Finally, variants are called with the pipeline, linking barcodes or flycodes with their respective protein variants.

Requirements

Local and cluster execution

Nextflow (Installation guide), on the cluster it has to be installed in a mamba/ conda environment called nextflow.
Mamba/ Conda (https://conda-forge.org/) ### Local execution only
Dorado (Installation guide). ### Cluster execution only
Slurm workflow manager
Singularity

Running the pipeline

Clone the repository with git clone https://github.com/fabianackle/NestLink-pipeline.git.
Create a params.json file with the parameters listed below, specify the nanopore reads (bam) and reference sequence, see the examples contained in this repo.
Run the pipeline with either ./run_NL-pipeline.sh for local execution or on a cluster with sbatch run_NL-pipeline.slurm.

Parameters

| Parameter | Type | Description | |---------------------------|----------------------|---------------------------------------------| | data | String | Path to input BAM file. | | reference | String | Path to reference FASTA file. | | filter_quality | Float | Minimum mean read quality threshold. | | filter_min_length | Integer | Read filtering minimum length threshold. | | filter_max_length | Integer | Read filtering maximum length threshold. | | extract_barcode_adapter | String | Linked adapter for barcode extraction. | | barcode_regex | String | Regular expression matching the barcode. | | medaka_dorado_model | String | Dorado model used for basecalling. | | barcode_pattern | List(String, String) | Sequences flanking the barcode. | | orf_pattern | List(String, String) | Sequences flanking ORF. | | translate_barcode | Boolean | Translates barcode, used with flycodes. | | outdir | String | Output directory for results. |

Owner

Name: Fabian Ackle
Login: fabianackle
Kind: user
Company: University of Zurich

Website: https://fabianackle.ch/
Twitter: f_ackle
Repositories: 1
Profile: https://github.com/fabianackle

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: NestLink-pipeline
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Fabian
    family-names: Ackle
    affiliation: University of Zurich
    orcid: 'https://orcid.org/0000-0002-7199-5004'
repository-code: 'https://github.com/fabianackle/NestLink-pipeline'
keywords:
  - NestLink
  - Barcode
  - Consensus
  - Nanopore
  - Workflow
  - Pipeline
license: MIT

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