https://github.com/boyle-lab/nanopal-and-cas9-targeted-enrichment-pipelines
The pipelines for the project 'Cas9 targeted enrichment of mobile elements using nanopore sequencing', including NanoPal and Cleavage-site analysis
https://github.com/boyle-lab/nanopal-and-cas9-targeted-enrichment-pipelines
Science Score: 23.0%
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Repository
The pipelines for the project 'Cas9 targeted enrichment of mobile elements using nanopore sequencing', including NanoPal and Cleavage-site analysis
Basic Info
- Host: GitHub
- Owner: Boyle-Lab
- Language: Shell
- Default Branch: main
- Size: 27.6 MB
Statistics
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Cas9 targeted enrichment of mobile elements using nanopore sequencing in human genomes
Nano-Pal pipeline for Nanopore reads from Flongle/MinION
Run for L1Hs
bash Nano-Pal.LINE.sh
Run for AluYb
bash Nano-Pal.AluYb.sh
Run for AluYa
bash Nano-Pal.AluYa.sh
Run for SVAF ``` bash Nano-Pal.SVAF.sh ```
Run for SVAE ``` bash Nano-Pal.SVAE.sh ```
Requires:
samtools/1.3.1 https://github.com/samtools/samtools
ncbi-blast++/2.10.0 ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
PALMER https://github.com/mills-lab/PALMER
minimap2 https://github.com/lh3/minimap2
Guide RNA design pipeline
We have included three bash files for guide RNA design: bash.alu.sh, bash.line1.sh, and bash.sva.sh in the RNA.design.pipelines folder.
We also included the consensus sequences for different categories of mobile elements used for the design in the lib folder.
Requires:
jellyfish/2.2.8
Guide RNA cleavage-site analysis
Run MEI_ONTreads_alignment.py to perform alignments.
Accepted mobile element names: L1HS, AluYa5, AluYb8, SVAE, SVAF
MEI_ONTreads_alignment.py {mobileElementName} {mobileElementSeq.fasta} {long_reads_input_file.fasta} {outfile.txt}
Requires:
import sys
import Bio
L1Hs methylation analysis
We have included two scripts for L1Hs methylation analysis: non_ref_pipeline.sh and reference_piepline.sh in the Methylation.pipelines folder.
Requires:
nanopolish https://github.com/jts/nanopolish
methylartist https://github.com/adamewing/methylartist
Citation
- Torrin L. McDonald, Weichen Zhou, Christopher Castro, Camille Mumm, Jessica A. Switzenberg, Ryan E. Mills, Alan P. Boyle,
Cas9 targeted enrichment of mobile elements using nanopore sequencing,
Nature Communications, 2021,
https://doi.org/10.1038/s41467-021-23918-y
For PALMER:
* Weichen Zhou, Sarah B Emery, Diane A Flasch, Yifan Wang, Kenneth Y Kwan, Jeffrey M Kidd, John V Moran, Ryan E Mills,
Identification and characterization of occult human-specific LINE-1 insertions using long-read sequencing technology,
Nucleic Acids Research, 2019, https://doi.org/10.1093/nar/gkz1173
Contact:
For Nano-Pal and others: arthurz@umich.edu or https://github.com/WeichenZhou
For cleavage-site anlaysis: castrocp@umich.edu or https://github.com/castrocp
For methylation analysis: crmumm@umich.edu or https://github.com/crmumm
Owner
- Name: The Boyle Lab
- Login: Boyle-Lab
- Kind: organization
- Email: apboyle@umich.edu
- Location: University of Michigan
- Website: http://BoyleLab.org
- Repositories: 10
- Profile: https://github.com/Boyle-Lab