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Title: GitHub - PombertLab/SSRG: The SSRG pipeline was created as a simple and focused tool to investigate genetic diversity between genomes.

Open Graph Title: GitHub - PombertLab/SSRG: The SSRG pipeline was created as a simple and focused tool to investigate genetic diversity between genomes.

X Title: GitHub - PombertLab/SSRG: The SSRG pipeline was created as a simple and focused tool to investigate genetic diversity between genomes.

Description: The SSRG pipeline was created as a simple and focused tool to investigate genetic diversity between genomes. - PombertLab/SSRG

Open Graph Description: The SSRG pipeline was created as a simple and focused tool to investigate genetic diversity between genomes. - PombertLab/SSRG

X Description: The SSRG pipeline was created as a simple and focused tool to investigate genetic diversity between genomes. - PombertLab/SSRG

Opengraph URL: https://github.com/PombertLab/SSRG

X: @github

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https://github.com/PombertLab/SSRG/blob/master/Images/logo.png
https://zenodo.org/doi/10.5281/zenodo.5532793
SSRG pipelinehttps://github.com/PombertLab/SSRG
SSRG.plhttps://github.com/PombertLab/SSRG/blob/master/SSRG.pl
get_SNPs.plhttps://github.com/PombertLab/SSRG/blob/master/get_SNPs.pl
Mashhttps://github.com/marbl/Mash
Ondov et al.https://pubmed.ncbi.nlm.nih.gov/27323842/
https://patch-diff.githubusercontent.com/PombertLab/SSRG#table-of-contents
Introductionhttps://patch-diff.githubusercontent.com/PombertLab/SSRG#Introduction
Requirementshttps://patch-diff.githubusercontent.com/PombertLab/SSRG#Requirements
Downloading from GitHubhttps://patch-diff.githubusercontent.com/PombertLab/SSRG#downloading-from-github
Installing dependencieshttps://patch-diff.githubusercontent.com/PombertLab/SSRG#installing-dependencies
Exampleshttps://patch-diff.githubusercontent.com/PombertLab/SSRG#Examples
Creating NCBI genome listshttps://patch-diff.githubusercontent.com/PombertLab/SSRG#Creating-NCBI-genome-lists
SSRG workflowhttps://patch-diff.githubusercontent.com/PombertLab/SSRG#SSRG-workflow
Mash workflowhttps://patch-diff.githubusercontent.com/PombertLab/SSRG#Mash-workflow
Misc scriptshttps://patch-diff.githubusercontent.com/PombertLab/SSRG#Misc-scripts
Funding and acknowledgmentshttps://patch-diff.githubusercontent.com/PombertLab/SSRG#Funding-and-acknowledgments
Referenceshttps://patch-diff.githubusercontent.com/PombertLab/SSRG#references
https://patch-diff.githubusercontent.com/PombertLab/SSRG#introduction
https://patch-diff.githubusercontent.com/PombertLab/SSRG#why-another-read-mapping-pipeline
single nucleotide polymorphismshttps://ghr.nlm.nih.gov/primer/genomicresearch/snp
insertions/deletionshttps://ghr.nlm.nih.gov/primer/mutationsanddisorders/possiblemutations
NCBI's SRAhttps://www.ncbi.nlm.nih.gov/sra
whole genome sequencinghttps://ghr.nlm.nih.gov/primer/testing/sequencing
SSRG.plhttps://github.com/PombertLab/SSRG/blob/master/SSRG.pl
https://patch-diff.githubusercontent.com/PombertLab/SSRG#deconstructing-genomes-into-synthetic-reads-has-the-following-advantages
Illuminahttps://www.illumina.com/
PacBiohttps://www.pacb.com/
Oxford Nanoporehttps://nanoporetech.com/
https://patch-diff.githubusercontent.com/PombertLab/SSRG#the-ssrg-pipeline-currently-can
NCBIhttps://www.ncbi.nlm.nih.gov/genome/browse#!/overview/
Mashhttps://github.com/marbl/Mash
https://patch-diff.githubusercontent.com/PombertLab/SSRG#requirements
Perl 5https://www.perl.org/
https://patch-diff.githubusercontent.com/PombertLab/SSRG#for-read-mapping
Samtoolshttp://www.htslib.org/
Minimap2https://github.com/lh3/minimap2
VarScan2http://dkoboldt.github.io/varscan/
Javahttps://www.java.com/
https://patch-diff.githubusercontent.com/PombertLab/SSRG#for-genetic-distance-estimations-with-mash
Mashhttps://github.com/marbl/Mash
Rhttps://www.r-project.org/
https://patch-diff.githubusercontent.com/PombertLab/SSRG#optional
Bowtie2http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
HISAT2https://ccb.jhu.edu/software/hisat2/index.shtml
NGMLRhttps://github.com/philres/ngmlr
BCFtoolshttp://samtools.github.io/bcftools/
https://patch-diff.githubusercontent.com/PombertLab/SSRG#downloading-from-github
VarScan2http://dkoboldt.github.io/varscan/
VarScan2http://dkoboldt.github.io/varscan/
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https://patch-diff.githubusercontent.com/PombertLab/SSRG#installing-dependencies
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https://patch-diff.githubusercontent.com/PombertLab/SSRG#examples
https://patch-diff.githubusercontent.com/PombertLab/SSRG#creating-ncbi-genome-lists
NCBIhttps://www.ncbi.nlm.nih.gov/genome/browse#!/overview/
https://github.com/PombertLab/SSRG/blob/master/Images/NCBI_g1.png
https://github.com/PombertLab/SSRG/blob/master/Images/NCBI_g2.png
https://github.com/PombertLab/SSRG/blob/master/Images/NCBI_g3.png
https://patch-diff.githubusercontent.com/PombertLab/SSRG#ssrg-workflow
https://patch-diff.githubusercontent.com/PombertLab/SSRG#a-case-example-with-minimap2-varscan2-and-3-streptococcus-pneumoniae-genomes
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https://patch-diff.githubusercontent.com/PombertLab/SSRG#mash-workflow
https://patch-diff.githubusercontent.com/PombertLab/SSRG#case-example-with-mash-r-and-75-streptococcus-pneumoniae-genomes
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S_pneumoniae_75_NJ_tree.pdfhttps://github.com/PombertLab/SSRG/blob/master/Images/S_pneumoniae_75_NJ_tree.pdf
Images/https://github.com/PombertLab/SSRG/tree/master/Images
MashR_plotter.plhttps://github.com/PombertLab/SSRG/blob/master/Tools/MASH/MashR_plotter.pl
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Images/https://github.com/PombertLab/SSRG/tree/master/Images
https://patch-diff.githubusercontent.com/PombertLab/SSRG#misc-scripts
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efetchhttps://dataguide.nlm.nih.gov/edirect/efetch.html
E-utilitieshttp://www.ncbi.nlm.nih.gov/books/NBK25499/
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queryNuccore.plhttps://github.com/PombertLab/SSRG/blob/master/Tools/NCBI/queryNuccore.pl
get_SRA.plhttps://github.com/PombertLab/SSRG/tree/master/Tools/NCBI
NCBI Sequence Read Archivehttps://www.ncbi.nlm.nih.gov/sra
NCBI SRA toolkithttps://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software
get_SRA.plhttps://github.com/PombertLab/SSRG/tree/master/Tools/NCBI
get_SRA.plhttps://github.com/PombertLab/SSRG/tree/master/Tools/NCBI
https://patch-diff.githubusercontent.com/PombertLab/SSRG#funding-and-acknowledgments
https://patch-diff.githubusercontent.com/PombertLab/SSRG#references
29750242https://pubmed.ncbi.nlm.nih.gov/29750242
PMC6137996https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6137996
10.1093/bioinformatics/bty191https://doi.org/10.1093/bioinformatics/bty191
33590861https://pubmed.ncbi.nlm.nih.gov/33590861
PMC7931819https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7931819
10.1093/gigascience/giab008https://doi.org/10.1093/gigascience/giab008
22388286https://pubmed.ncbi.nlm.nih.gov/22388286
PMC3322381https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322381
10.1038/nmeth.1923https://doi.org/10.1038/nmeth.1923
25751142https://pubmed.ncbi.nlm.nih.gov/25751142
PMC4655817https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4655817
10.1038/nmeth.3317https://doi.org/10.1038/nmeth.3317
29713083https://pubmed.ncbi.nlm.nih.gov/29713083
PMC5990442https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5990442
10.1038/s41592-018-0001-7https://doi.org/10.1038/s41592-018-0001-7
19505943https://pubmed.ncbi.nlm.nih.gov/19505943
PMC2723002https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723002
10.1093/bioinformatics/btp352https://doi.org/10.1093/bioinformatics/btp352
22300766https://pubmed.ncbi.nlm.nih.gov/22300766
PMC3290792https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3290792
10.1101/gr.129684.111https://doi.org/10.1101/gr.129684.111
26826718https://pubmed.ncbi.nlm.nih.gov/26826718
PMC4892413https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4892413
10.1093/bioinformatics/btw044https://doi.org/10.1093/bioinformatics/btw044
27323842https://pubmed.ncbi.nlm.nih.gov/27323842
PMC4915045https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4915045
10.1186/s13059-016-0997-xhttps://doi.org/10.1186/s13059-016-0997-x
URLhttps://www.r-project.org/
1301.3342v2https://arxiv.org/abs/1301.3342
URLhttps://jmlr.csail.mit.edu/papers/volume9/vandermaaten08a/vandermaaten08a.pdf
snps https://patch-diff.githubusercontent.com/topics/snps
genetic-distance-estimations https://patch-diff.githubusercontent.com/topics/genetic-distance-estimations
fastq-datasets https://patch-diff.githubusercontent.com/topics/fastq-datasets
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MIT license https://patch-diff.githubusercontent.com/PombertLab/SSRG#MIT-1-ov-file
Please reload this pagehttps://patch-diff.githubusercontent.com/PombertLab/SSRG
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