seqyclean

[…] For the shotgun metagenomic dataset, overlapping reads were paired using PEAR 0.9.5 () and filtered for quality with Phred > 30, and a length longer than 80 nt using Seqyclean 1.9.8. The reads were annotated by BLASTX against the NCBI-nr database (November 2016) using DIAMOND (). Retrieved annotations were later analyzed using MEGAN6 (). The data presented in the […]

[…] First, the quality of the sequencing reads was checked with FastQC tool []. Read quality trimming was performed using SeqyClean tool (v.1.3.12) [] to select reads with average Phred score quality ≥ 24 and minimum length of 65 bp. The reads were aligned against the Gallus_gallus-4.0 chicken reference genome [] using B […]

[…] GenBank SRA (PRJNA407969). We screened all shotgun reads to eliminate sequencing adapters, identify and remove contaminants, and trim reads based on quality scores using the bioinformatics pipeline “SeqyClean.py” provided by the IBEST Computational Resources Core. We assembled the remaining shotgun reads into contigs using Newbler v.2.6. We also included published shotgun sequence data for an add […]

[…] from the male and female genome builds (accessions SRX180259, SRX180261, and SRX180262) to identify putative X, Y and autosomal scaffolds using relative sequencing coverage between the sexes. We used SeqyClean version 1.8.10 to quality filter, adapter trim, and screen for common Acinetobacter contaminants (accessions CP000521, ACPN01000000). Filtered reads were then mapped to the reference male ge […]

[…] Raw sequences were trimmed for adaptors and low quality using SeqyClean v1.3.12. (https://github.com/ibest/seqyclean) using 26 Phred quality parameter for maximum average error and a fasta file with contaminant sequences from the Univec database (https://www.ncb […]

[…] na, San Diego, CA, United States). Prior to analysis, duplicate read pairs were removed using a custom Python script. Sequencing adapters and low-quality bases were removed using the software package Seqyclean. All remaining reads were mapped to the chromosome of either E. coli O157:H7 (BA000007.2) or P. putida KT2442 (NC_002947.3) using Bowtie2. The unused reads (i.e., non-chromosomal reads) were […]