PRINSEQ

[…] an illumina miseq platform using a 250-bp paired-end format, resulting in a total of 5,320,190 reads. the raw sequences were preprocessed using cutadapt version 1.14 to trim adaptors (10) and using prinseq version 0.20.4 to perform quality filtering (11). initial genome assembly was performed with the spades version 3.10.0 genome assembler program (12). contigs less than 1,000 bp in length […]

[…] illumina gaiix at the exeter sequencing service producing 2× 212 760 559 hiseq reads along with 2× 15 266 599 and 2× 16 274 715 gaiix reads. after trimming and cleaning (using tagcleaner [128] and prinseq [129]) of the data, we subsequently digitally normalized it with khmer [130] in order to discard redundant data and sampling variation and remove errors. this reduced the number of reads […]

[…] control of contamination., bioinformatic pre-processing of the viral metagenomes was performed as follows. fastq-format files containing raw sequence reads, were quality and length- filtered using prinseq-lite (v0.20.4) [18], which also implemented the removal of reads containing polynucleotide tails, ns and low complexity sequences. next, trimmed reads showing average quality below 20 […]

[…] concentration of 1.5nm and sequenced on an illumina® nextseq 500 using 150bp paired end kit as per manufacturer’s instructions. see also key resources table., raw reads were initially processed with prinseq-lite v0.20.4 (schmieder and edwards, 2011) to trim low-quality reads. they were further aligned with tophat2 v2.0.11 (kim et al., 2013) on the grch37 human assembly and fpkm values […]

[…] ultra-high-throughput sequencing system (illumina) using paired-ends (2 × 250 bp) for 500 cycles as per the manufacturers’ instructions., raw reads were quality-filtered, trimmed and screened using prinseq-lite v0.20.4 [29] in combination with in-house scripts. we used flash v1.2.11 (fast length adjustment of short reads) to align high-quality paired-end reads [30]. sequences were de novo […]