/NGS

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NGS

Some usefule Resources are listed below based on their usage.

Micro-Rna Analysis

  1. http://bcb.io/2016/03/24/mirqc/

  2. http://srna-workbench.cmp.uea.ac.uk/the-small-rna-workbench-version-4-3-1/

  3. DIANA Tools

  4. MirPath 3

  5. https://omictools.com/workflows-pipelines4-category

Published Pipelines

  1. systemPipeR: NGS workflow and report generation environment. [HTML] (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1241-0), Bioconductor

  2. https://peerj.com/articles/4466/?utm_source=summary_email_publication&utm_medium=email&utm_campaign=connection https://github.com/oscar-franzen/rnaed.git

  3. https://github.com/alesssia/YAMP

  4. http://qiime.org/

  5. https://f1000research.com/slides/6-1185

https://www.nextflow.io/example4.html 6. https://www.frontiersin.org/articles/10.3389/fcell.2014.00070/full

Metagenomics

  1. https://www.sciencedirect.com/science/article/pii/S0168165617315985

  2. https://usegalaxy.org/u/aun1/p/windshield-splatter

  3. FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies

  4. http://clovr.org/methods/clovr-metagenomics/

  5. https://arxiv.org/ftp/arxiv/papers/1604/1604.04103.pdf

  6. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0169563

  7. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4426941/

  8. https://github.com/CSB5/shotgun-metagenomics-pipeline

  9. https://www.nature.com/articles/srep23774

  10. https://github.com/jamesabbott/SCaMP