KO | EN

GitLite

Minimalist Open Source Repository Search Engine

gitlite — search

#dsh #dsh-plugin #developer-tools #ai-agent #claude-code #codex #typescript #ai-agents #deepseek-harness #mcp #cli #rust

GBS-SNP-CROP

★ 33 Open GitHub ↗

GBS SNP Calling Reference Optional Pipeline

// repository documentation

Was this content helpful?

★ 0 (0 ratings)

# GBS-SNP-CROP

### *Latest release v.4.1 (October 6, 2019)*

### Introduction
The **GBS** **SNP** **C**alling **R**eference **O**ptional **P**ipeline (GBS-SNP-CROP) is executed via a sequence of [seven Perl scripts][4] that integrate custom parsing and filtering procedures with well-known, vetted bioinformatic tools, giving the user full access to all intermediate files. By employing a novel strategy of variant (SNPs and indels) calling based on the correspondence of within-individual to across-population patterns of polymorphism, the pipeline is able to identify and distinguish high-confidence variants from both sequencing and PCR errors, whether or not a reference genome is available. In the latter case, the pipeline adopts a clustering strategy to build a population-tailored "Mock Reference" using the same GBS data for downstream calling and genotyping. Designed for libraries of either paired-end (PE) or single-end (SE) reads of arbitrary lengths, GBS-SNP-CROP maximizes data usage by eliminating unnecessary data culling due to imposed length uniformity requirements. GBS-SNP-CROP is a complete bioinformatics pipeline developed primarily to support curation, research, and breeding programs wishing to utilize GBS for the cost-effective genome-wide characterization of plant genetic resources.

### Pipeline workflow
**Stage 1. Process the raw GBS data**  
- *Step 1: Parse the raw reads*  
- *Step 2: Trim based on quality and adaptors*  
- *Step 3: Demultiplex*

**Stage 2. Build the Mock Reference**   
- *Step 4: Cluster reads and assemble the Mock Reference*

**Stage 3. Map the processed reads and generate standardized alignment files**  
- *Step 5: Align with BWA-mem and process with SAMtools*  
- *Step 6: Parse mpileup outputs and produce the variants discovery matrix*

**Stage 4. Call Variants and Genotypes**  
- *Step 7: Filter variants and call genotypes*

**PLEASE NOTE: GBS-SNP-CROP is an intentionally modular and flexible pipeline. If your data are already demultiplexed and filtered, simply skip Stage 1 and enter the pipeline at Stage 2. If you have a reference genome and no need for a Mock Reference, simply skip Stage 2 and go directly to Stage 3. Refer to the [User Manual][2] for input file naming conventions for each Step.**

Below is a schematic of the workflow, with inputs and outputs (boxes) indicated for each Step (arrows). 
![](https://github.com/halelab/GBS-SNP-CROP/blob/master/images/workflow.jpg)

### Released versions
[v.4.1][19]: Released on 10/6/2019  
[v.4.0][18]: Released on 10/22/2018  
[v.3.0][16]: Released on 2/8/2018  
[v.2.0][14]: Released on 2/22/2017  
[v.1.1][13]: Released on 3/11/2016  
[v.1.0][12]: Released on 1/12/2016

### Getting Help
Begin by carefully going through the [GBS-SNP-CROP User manual][2]. Before posting a question or starting a discussion, please first refer to the [FAQ page][17]. Also, please check your barcode ID file for empty characters or blank spaces and verify that it was saved as a tab-delimited file. If you're still facing an issue or have suggestions for improving this tool, kindly submit your question or comment to our [Google groups page][5].

### Requirements
* [Java 7 or higher][6] - The latest version of GBS-SNP-CROP (v.4.1) was tested using Java 8 (update 221)
* [Trimmomatic][7] Latest version tested using v.0.39 (Bolger et al., 2014)
* [PEAR][8] Latest version tested with v.0.9.11 (Zhang et al., 2014)
* [VSEARCH][9] Latest version tested with v2.13.7 (Rognes et al., 2016)
* [BWA aligner][10] Latest version tested with v.0.7.12 (Li & Durbin, 2009)
* [SAMTools][11] Latest version tested with v.1.7 (Li et al., 2009)
* The following five [CPAN modules][20] also need to be installed: Getopt::Long, IO::Zlib, List::Util, List::MoreUtils, Parallel::ForkManager

### Citing GBS-SNP-CROP
[Melo et al. GBS-SNP-CROP: A reference-optional pipeline for SNP discovery and plant germplasm characterization using genotyping-by-sequencing data. BMC Bioinformatics. 2016. 17:29. DOI 10.1186/s12859-016-0879-y.][1]

[1]:https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-0879-y
[2]:https://github.com/halelab/GBS-SNP-CROP/wiki/GBS-SNP-CROP-User-Manual-(v.4.1)
[3]:http://www.halelab.org
[4]:https://github.com/halelab/GBS-SNP-CROP/tree/master/GBS-SNP-CROP-scripts
[5]:https://groups.google.com/forum/#!forum/gbs-snp-crop
[6]:https://www.java.com/en/
[7]:http://www.usadellab.org/cms/?page=trimmomatic
[8]:https://www.h-its.org/en/research/sco/software/#NextGenerationSequencingSequenceAnalysis
[9]: https://github.com/torognes/vsearch
[10]:http://bio-bwa.sourceforge.net
[11]:http://samtools.sourceforge.net
[12]:https://github.com/halelab/GBS-SNP-CROP/releases/tag/v.1.0
[13]:https://github.com/halelab/GBS-SNP-CROP/releases/tag/v.1.1
[14]:https://github.com/halelab/GBS-SNP-CROP/releases/tag/v.2.0
[15]:http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf
[16]:https://github.com/halelab/GBS-SNP-CROP/releases/tag/v.3.0
[17]:https://github.com/halelab/GBS-SNP-CROP/wiki/Frequently-Asked-Questions-(FAQs)
[18]:https://github.com/halelab/GBS-SNP-CROP/releases/tag/v.4.0
[19]:https://github.com/halelab/GBS-SNP-CROP/releases/tag/v.4.1
[20]:http://www.cpan.org/modules/index.html

GBS-SNP-CROP

Explore Similar Repositories

Was this content helpful?

Recent Feedback

Download README