SCVUR_16S_metabarcode_pipeline | Data flow to process 16S metabarcodes

by terrimporter Perl Version: v.3.0.1 License: No License

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kandi X-RAY | SCVUR_16S_metabarcode_pipeline Summary

SCVUR_16S_metabarcode_pipeline is a Perl library. SCVUR_16S_metabarcode_pipeline has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

This pipeline begins with raw paired-end Illumina MiSeq fastq.gz files. Reads are paired. Primers are trimmed. All the samples are pooled for a global analysis. Reads are dereplicated and denoised producing a reference set of exact sequence variants (ESVs). These ESVs are taxonomically assigned using the 16S reference set available with the RDP Classifier (Wang et al., 2007) available from . This data flow has been developed using a conda environment and snakemake pipeline for improved reproducibility. It will be updated on a regular basis so check for the latest version at

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Support

SCVUR_16S_metabarcode_pipeline has a low active ecosystem.

It has 2 star(s) with 0 fork(s). There are no watchers for this library.

It had no major release in the last 12 months.

SCVUR_16S_metabarcode_pipeline has no issues reported. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of SCVUR_16S_metabarcode_pipeline is v.3.0.1

Quality

SCVUR_16S_metabarcode_pipeline has 0 bugs and 0 code smells.

Security

SCVUR_16S_metabarcode_pipeline has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

SCVUR_16S_metabarcode_pipeline code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

SCVUR_16S_metabarcode_pipeline does not have a standard license declared.

Check the repository for any license declaration and review the terms closely.

Without a license, all rights are reserved, and you cannot use the library in your applications.

Reuse

SCVUR_16S_metabarcode_pipeline releases are available to install and integrate.

Installation instructions are not available. Examples and code snippets are available.

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SCVUR_16S_metabarcode_pipeline Key Features

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SCVUR_16S_metabarcode_pipeline Examples and Code Snippets

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Vulnerabilities

No vulnerabilities reported

Install SCVUR_16S_metabarcode_pipeline

You can download it from GitHub.

Support

Instead of continually traversing nested directories to get to files, I create symbolic links to target directories in a top level directory. Symbolic links can also be placed in your ~/bin directory that point to scripts that reside elsewhere on your system. So long as those scripts are executable (e.x. chmod 755 script.plx) then the shortcut will also be executable without having to type out the complete path or copy and pasting the script into the current directory. This can be especially useful so that you don't have to maintain multiple copies of large raw read files in different places.

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