QuasiRecomb

[…] had a mean coverage of >10 following alignment with the zikv reference genome (genbank accession number kj776791.2) used in this study. the frequencies of minor variants were calculated using quasirecomb (). sequences of individual viral proteins were compared to the protein data bank using the online ncbi protein blast server (https://blast.ncbi.nlm.nih.gov/blast.cgi?page=proteins)., […]

[…] calling was performed using a codon-level approach with an in-house pipeline. amino acid variants were flagged if associated with hla footprints specific for the patient’s hla class i genotype. quasirecomb [] software was used to obtain nucleotide positional entropy values and to reconstruct full gag haplotype sequences. mean entropy values were calculated for gag epitopes coordinates […]

[…] relevant statistics (supplemental presentation ). major nucleotide variants were called using clc genomics workbench and their frequencies sampled and extracted using samtools (supplemental table ). quasirecomb version 1.2 () was used to reconstruct the viral haplotypes from sequencing data in bam files. local haplotype reconstruction across genes was performed using the default setting […]

[…] paired-end reads., for each time point, the sequence reads were mapped to the hrsv-a2 genome by using bowtie2. for each alignment to the hrsv genome, the output bam files were further analyzed using quasirecomb (). while bowtie2 aligned more than 1 million reads to the hrsv genome, we selected 1 million alignments at random. we used the coverage option for quasirecomb (command line java − […]

[…] sequencing errors., http://sourceforge.net/projects/viquas/ , a number of unsupervised quasispecies spectrum reconstruction (qsr) methods such as shorah [], qure [], predicthaplo [], vispa [] and quasirecomb [] are available in literature. comprehensive reviews on these methods are presented in [] and []. we recently formulated a novel unsupervised method named viquas [] for qsr and showed […]