PRINSEQ

[…] es were trimmed to remove Illumina adapters using Cutadapt version 1.2.1 with option -O 3 () and Sickle version 1.200 with a minimum quality score of 20 (). Further quality control was performed with Prinseq-lite () with the following parameters: minimum read length of 35, GC percentage between 5 and 95%, minimum mean quality of 25, dereplication (removal of identical reads, leaving 1 copy), and r […]

[…] ew England BioLabs) and sequenced on Illumina HiSeq 4000 using 50 bp single-read chemistry.Raw ChIP-seq reads were evaluated with FastQC (version 0.11.4). Quality-filtering and trimming was done with PRINSEQ-lite (version 0.20.4). Resulting high-quality reads were simultaneously mapped against the Mus musculus (GRCm38) and Drosophila melanogaster (dm6) reference genomes via BWA (version 0.7.15). S […]

[…] are deposited in the NCBI database within the Bioproject PRJNA380214 under the SRA study SRP133552.Prior to metagenomic analysis, sequence reads with a quality score mean below 30 were removed using Prinseq []. The 16S rRNA sequence analysis was performed using Mothur v. 1.39 []. Analysis was performed as according to the MiSeq SOP (accessed online 28/06/2017; []). The 16S rRNA gene sequences wer […]

[…] gent Kit v3 (600 Cycles) (Illumina K.K., Tokyo).The nucleotides with a quality value (QV) <30 in the 3′ terminal and the adapter-index sequence in the 5′ terminal were trimmed from the MiSeq reads by PRINSEQ v0.20.4, and those shorter than 200 bp were excluded. After the quality filtering, an overlap fragment of the 300-bp-paired reads (read 1 and read 2) were constructed by using COPE v1.1.3 with […]

[…] e genomes to remove host and any contaminant sequences. The de-multiplexed reads were trimmed to remove primers and adaptors and filtered to exclude short reads and those with low complexity regions (Prinseq v0.20.2, minimum quality mean = 30, max Ns = 20). A total of 512 million reads remained in the dataset after host subtraction and quality filtering (Average reads per sample = 27 million; rang […]

[…] (http://hannonlab.cshl.edu/fastx_toolkit/), which provides a number of functions to accomplish all of these steps. Other alternatives, with more limited functions include Cutadapt [], Trimmomatic [], PRINSEQ [] as well as custom scripts.Mapping to reference genomes: The reads that pass the above filtering steps are mapped onto reference genomes or transcriptomes. The most commonly used mapping alg […]