Tag: PhiX
High-quality single amplicon sequencing method for illumina MiSeq platform using pool of ‘N’ (0-10) spacer-linked target specific primers without PhiX spike-in
Background: Illumina sequencing platform requires base diversity in the initial 11 cycles for efficient cluster identification and colour matrix estimation. This limitation yields low-quality data for amplicon libraries having homogeneous base composition. Spike-in of PhiX library ensures base diversity but reduces the overall number of sequencing reads for data analysis….
Failed to calculate read length
fastq_screen error: Failed to calculate read length 1 Running it like this: fastq_screen –conf $FASTQ_SCREEN_DATA/fastq_screen.conf –aligner bowtie2 –threads 6 03dpf.filtered.tagged.unmapped-1.fasta.gz Runs into this error. I cannot seem to find any information about this. Using fastq_screen v0.15.1 Reading configuration from ‘/FastQ_Screen_Genomes/fastq_screen.conf’ Adding database Human Adding database Mouse Adding database Rat Adding…
Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils
1. Introduction Soil harbors high abundance and diversity of prokaryotic microorganisms, with 1 g of soil containing up to 10 billion microbial cells (Torsvik and Øvreås, 2002) and 103–106 phylotypes (Bickel and Or, 2020), including many microorganisms that play critical biogeochemical roles (Crowther et al., 2019). With continuous expansion of prokaryotic…
Characterization of antibiotic resistomes by reprogrammed bacteriophage-enabled functional metagenomics in clinical strains
This research complies with all relevant ethical regulations approved by the Human Investigation Review Board of Albert Szent-Györgyi Clinical Centre of the University of Szeged and the National Biodiversity Authority (NBA) of India. Permission for the faecal sample collection was obtained from the Human Investigation Review Board of Albert Szent-Györgyi…
Systematic and benchmarking studies of pipelines for mammal WGBS data in the novel NGS platform | BMC Bioinformatics
Comparison of read level and improving the mapping efficiency according to trimming Since the generation of high-quality WGBS data ultimately impacts the quantification and interpretation of Cs methylation levels, it is indispensable to monitor the raw data quality and interrogate the appropriate pre-processing step to cleanse data [1]. To avoid…
