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lacto_genome

Progress on the Lactococcus strain PrHT3

https://github.com/hoytpr/lacto_genome

Science Score: 18.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
    Found CITATION.cff file
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    codemeta.json file
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    .zenodo.json file
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    DOI references
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    Academic publication links
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    Academic email domains
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    Scientific vocabulary similarity
    Low similarity (4.6%) to scientific vocabulary

Keywords

genome-assembly
Last synced: 10 months ago · JSON representation ·

Repository

Progress on the Lactococcus strain PrHT3

Basic Info
  • Host: GitHub
  • Owner: hoytpr
  • Language: CSS
  • Default Branch: main
  • Homepage:
  • Size: 2.49 MB
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Topics
genome-assembly
Created about 5 years ago · Last pushed over 3 years ago
Metadata Files
Readme Citation

README.md

The Draft Genome of Lactococcus lactis str. PrHT3

Process/Pipeline

General Description is on the Project page.

These data were submitted to NCBI and used the INSDC standards for genome assembly submission.

The bioinformatics of this project will be placed in Metadata, and we provide a project-specific bash script for reproducibility. The use of the CheckM software to validate the species is within the Validate page which includes the brief set of commands to generate the phylogenetic tree and statistics.

We are grateful to the authors of the sofware used. Citations and acknowledgements

Owner

  • Name: Pete
  • Login: hoytpr
  • Kind: user
  • Company: Oklahoma State University

Older gene expression specialist and molecular geneticist. Data skills in progress. Bioinformatics/Genomics champion to Life Scientists. @thecarpentries

Citation (citations.md) 

---
---

## Citations

It is very important to recognize the work of those that make these analyses possible
and provide their work for free. Our analyses were built upon the following software:

<a name="cit01"></a>
### QUAST

Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi and Glenn Tesler,
QUAST: quality assessment tool for genome assemblies,
Bioinformatics (2013) 29 (8): 1072-1075. doi: 10.1093/bioinformatics/btt086
First published online: February 19, 2013 

https://github.com/ablab/quast

<a name="cit02"></a>
### Trimmomatic

Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114-2120.

https://github.com/usadellab/Trimmomatic

<a name="cit03"></a>
### FastQC

Bioinformatics, B. Babraham Institute; Cambridge, UK: 2011. FastQC: A Quality Control Tool for High Throughput Sequence Data.

https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

<a name="cit04"></a>
### SPAdes

Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., ... & Pevzner, P. A. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of computational biology, 19(5), 455-477.

https://github.com/ablab/spades

<a name="cit05"></a>
### Blast

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of molecular biology, 215(3), 403-410.

https://blast.ncbi.nlm.nih.gov/Blast.cgi

<a name="cit06"></a>
### Bandage

Wick, R. R., Schultz, M. B., Zobel, J., & Holt, K. E. (2015). Bandage: interactive visualization of de novo genome assemblies. Bioinformatics, 31(20), 3350-3352.

https://rrwick.github.io/Bandage/

<a name="cit07"></a>
### Bowtie 2

Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature methods, 9(4), 357.

https://github.com/BenLangmead/bowtie

<a name="cit08"></a>
### SAMtools 

Twelve years of SAMtools and BCFtools
Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li
GigaScience, Volume 10, Issue 2, February 2021, giab008, https://doi.org/10.1093/gigascience/giab008

https://github.com/samtools/samtools

<a name="cit09"></a>
### BBTools

Bushnell B, Rood J, Singer E (2017) BBMerge – Accurate paired shotgun read merging via overlap. PLoS ONE 12(10): e0185056. https://doi.org/10.1371/journal.pone.0185056

https://sourceforge.net/projects/bbmap/

### CheckM

Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research, 25: 1043–1055.

https://github.com/Ecogenomics/CheckM/wiki

### Dendroscope

D.H. Huson and C. Scornavacca, Dendroscope 3- An interactive viewer for rooted phylogenetic trees and networks, Systematic Biology (2012); doi: 10.1093/sysbio/sys062

https://software-ab.informatik.uni-tuebingen.de/download/dendroscope3/welcome.html

| [To README Page](/README.md) | [To metadata page](/metadata.md) | [To scripts page](/files/lactoscript-only.sh) |
| --- | --- | --- |

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