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nf-core-miniranger

https://github.com/sychen9584/nf-core-miniranger

Science Score: 57.0%

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Repository

Basic Info
  • Host: GitHub
  • Owner: sychen9584
  • License: mit
  • Language: Nextflow
  • Default Branch: main
  • Size: 35.2 MB
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Created about 1 year ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

nf-core/miniranger

Nextflow run with conda run with docker run with singularity nf-test

Introduction

nf-core/miniranger is a lightweight bioinformatics pipeline that can be used to analyse single cell RNA sequencing (scRNA-seq) utilizing mainly [simpleaf(https://simpleaf.readthedocs.io/en/latest/index.html)]. simpleaf is a rust framework that simplifies the processing of single cell data using tools from the [alevin-fry(https://alevin-fry.readthedocs.io/en/latest/)] ecosystem. The pipeline takes a samplesheet, FASTQ files, and reference genome FASTA and annotation (gtf) files as input. It performs quality control (QC) and pseudoalignment, and produces a cell x gene expression matrix and QC report as output.

```mermaid

%% https://xkcd.com/1195/

graph LR

A[[FASTQ files]] --> B1(FastQC) B1 --> C1(simpleaf quant) B2[[Reference genome
FASTA + GTF files]] --> C2(simpleaf index) C2 --> C1 C1 --> D1(AlevinQC) C1 --> D2(MultiQC) C1 --> D3[[Cell X Gene matrix]] D1 --> E[[QC reports]] D2 --> E

```

  1. Read QC (FastQC)
  2. Index reference genome (simpleaf index)
  3. Pseudo-alignment (simpleaf quant)
  4. QC report for raw reads (MultiQC)
  5. QC report for simpleaf (alevinQC)

Usage

[!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

csv sample,fastq_1,fastq_2 PBMC_1k,PBMC_1k_S1_L001_R1_001.fastq.gz,PBMC_1k_S1_S1_L002_R2_001.fastq.gz

Each row represents a fastq file (single-end) or a pair of fastq files (paired end). Rows with the same sample identifier are considered technical replicates and merged automatically.

Now, you can run the pipeline using:

bash nextflow run nf-core/miniranger \ -profile <docker/singularity/conda/test> \ --input samplesheet.csv \ --outdir <OUTDIR> \ --fasta genome.fa \ --gtf genes.gtf --chemistry 10xv3

[!WARNING] Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Citations

nf-core-miniranger was originally developed by Sam Chen

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.

Owner

  • Login: sychen9584
  • Kind: user

Citation (CITATIONS.md) 

# nf-core/miniranger: Citations

## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)

> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

## Pipeline tools

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)

  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)

  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)

  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

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