Hello, I'm using HASLR with nanopore and Illumina data to assemble a P. falciparum genome.
All nanopore data has around ~50x coverage.
All Illumina short reads are set as 2 paired-end fastq files (the paired-end doesn't matter for haslr, I believe?)
I used this command: haslr.py -t 10 -o pfalciparum -g 23m -l nanopore_data.fasta nanopore -s illumina_data.fasta
The resulting asm.final.fa contains about 10 million base pairs, which is much shorter than the expected 23 million base pairs for plasmodium falciparum. I've run this on several different nanopore samples and gotten the same result: a much shorter assembly than expected.
Do you have any suggestions? Thank you so much.
Hello, I'm using HASLR with nanopore and Illumina data to assemble a P. falciparum genome.
All nanopore data has around ~50x coverage.
All Illumina short reads are set as 2 paired-end fastq files (the paired-end doesn't matter for haslr, I believe?)
I used this command: haslr.py -t 10 -o pfalciparum -g 23m -l nanopore_data.fasta nanopore -s illumina_data.fasta
The resulting asm.final.fa contains about 10 million base pairs, which is much shorter than the expected 23 million base pairs for plasmodium falciparum. I've run this on several different nanopore samples and gotten the same result: a much shorter assembly than expected.
Do you have any suggestions? Thank you so much.