Chun Shen Lim, Vitina Sozzi, Margaret Littlejohn, Lilly K.W. Yuen, Nadia Warner, Brigid Betz-Stablein, Fabio Luciani, Peter A. Revill, Chris M. Brown. (2020). Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypes. Microbial Genomics. DOI:10.1099/mgen.0.000492
Requirements
Most tools can be installed using conda or pip
- https://github.com/lh3/minimap2
- https://github.com/BrooksLabUCSC/flair
- https://github.com/bartongroup/2passtools
- https://github.com/relipmoc/skewer
- https://github.com/alexdobin/STAR
- https://github.com/samtools/samtools
- https://github.com/gpertea/stringtie
- https://github.com/broadinstitute/picard
- https://github.com/ENCODE-DCC/kentUtils
- https://github.com/arq5x/bedtools
- https://github.com/gpertea/gffcompare
- https://github.com/Kingsford-Group/rnaseqtools
- http://hollywood.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html
- https://github.com/WebLogo/weblogo
- https://github.com/brentp/pyfasta
- https://mafft.cbrc.jp/alignment/software/
- https://bioconductor.org/packages/release/bioc/html/Gviz.html
- https://bioconductor.org/packages/release/bioc/html/DESeq2.html
- https://cran.r-project.org/web/packages/tidyverse/index.html
- https://zlib.net/pigz/
- https://www.gnu.org/software/datamash/
Reference genomes and annotations
- http://hgdownload.soe.ucsc.edu/goldenPath/hg19/chromosomes/
- ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz
- HBV pgRNA sequences in the ref directory