Comments (1)
For k-mer counting with jellyfish, PanGenie per default uses a kmer size of 31, a hash size of 3,000,000,000, a counter length of 7, the maximum number of reprobes is 126 and kmers are represented in canonical representation. Also, PanGenie counts only kmers present in the graph it internally generates from the VCF. So I think running jellyfish like shown below should give the same results for kmer counting:
jellyfish count -m 31 -s 3G -p 126 -c 7 -C -L 1 --if <path-segments.fasta> <input.fasta>
Here, "path-segments.fasta" is a file PanGenie produces for its k-mer counting (output as <prefix>_path-segments.fasta
when running PanGenie). It contains all sequences present in the graph. At some point I have implemented the command
PanGenie-graph -r <reference.fa> -v <variants.vcf> -o <output-prefix>
which can be used to generate this file only (instead of running the whole kmer counting and genotyping). So you can try running this first to generate the file containing all graph sequences, and then run jellyfish using the result for parameter --if.
So far, I always directly used the reads as input to PanGenie instead of generating the jf file first, so unfortunately, I never compared sizes of jf/fastq files. What I have done in the past in order to reduce reads in fastq format, is to convert it to fasta (without qualities), as PanGenie does not use any base quality information.
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Related Issues (20)
- Feature request: support kff input files HOT 4
- Phasing HOT 1
- Using PanGenie for non-directed acyclic graph and pair-end reads HOT 1
- Error for PanGenie-index HOT 3
- .cereal cannot be opened HOT 1
- The vcfhub remove about 300Mb data in a 2.5Gb genome HOT 5
- The best method to use the genotyping-pipelines and the vcf-merging to quality control HOT 4
- How to retain only the STRUCTURE VARIATION for pangenie HOT 2
- The different sample with different lines in vcf HOT 3
- what is the role of unique kmers of overhang? HOT 1
- since alleles contain undefined nucleotides HOT 1
- pangenome-graph-from-assemblies not working for latest Pangenie HOT 1
- pangenie-index failed: std::runtime_error, "Hash full" HOT 3
- How to handle N bases in VCF-input files HOT 2
- lower SNP overlap rate between call set and GATK results. HOT 2
- Update catch2 to support glibc >2.33
- GraphBuilder: number of paths is limited to 254 in current implementation. HOT 3
- Genotype personalized pangenome HOT 4
- variation number HOT 1
- Issue with VCF (does not represent a pangenome graph)
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