gauravearn/pacbiohifi-analyzer

a pacbiohifi analyzer for pacbiohifi reads from sequence analysis to the graph alignments

pacbiohifi-analyzer

• a pacbiohifi analyzer for the pacbio hifi reads and gives all the information for the pacbiohifi reads from raw to the graph alignments.
• class functions include from reading, plotting, clipping, reading bam, generating the graphs, extracting the graph sequences, graph edges, splcier function for graphs.
• graph plotting is enabled using the ruby-charts
• initiate the class as

# class initialize or the gem initialize
- pacbiohi = PACBIOHIFIANALYZER.new("samplepacbiohifi.fastq")
# will read and make the index for the PacBiohifi
- pacbiohifi.makeindex
# will give you a tab delimited file for the PacBiohifi
- pacbiohifi.getLength
# will give you the fasta file for the PacBiohifi
- pacbiohifi.getFasta
# provide the graph start and end nodes and it will clip the pacbiohifi aligned for those edges
- pacbiohifi.graphextract
# will print the default PacBiohifi clippers
- pacbiohifi.getClippattern 
# you can define a new txt file containing the clipping patterns
- pacbiohifi.setClipper 
# clips the sequences of the specific positions and write the revised fasta.
- pacbiohifi.clipper
# search for the specific patterns in the PacBiohifi reads 
- pacbiohifi.search
# align the reads to the genome for the pangenome construction. 
# provide the directory path containing the genome file ending in the .fasta and the protein files ending in the .fa, 
# if the option is writecommand, it will output a shell compatible run script for the 
# high performance computing and if the option is commandrun then it will run the alignment. 
- pacbiohifi.pacbioalign(dirpath) 
# pacbio splicer: added a new function which will read the pacbiohifi aligned reads and 
# for each of the reads aligned will extract the corresponding sequences, and if given will match them with the annotated regions.
-pacbiohifi.pafslicer(alignedfile, fastafile)

• gem due to release 2024-5-15 and can be installed as

gem install pacbio-hifianalyzer

Gaurav
Academic Staff Member
Bioinformatics
Institute for Biochemistry and Biology
University of Potsdam
Potsdam,Germany