seqyclean

[…] on library preparation and sequencing can be obtained from moreira et al. []., 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 […]

[…] v3 (600 cycles) (illumina)., 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 […]

[…] 0.10.1) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). all reads were filtered for phred quality (qs) 23 (sequence inside) and 30 (sequence edges) and minimum length of 65 bp using the seqyclean software (v.1.9.9) (https://github.com/ibest/seqyclean). the same package was also used to remove contaminant sequences (primers and vectors) using the univec database […]

[…] and validated using the bioanalyzer. paired-end sequencing of 101 bp reads was performed using the illumina hiseq 2000 (ampulla samples) and illumina hiseq 2500 (isthmus samples) platforms. using seqyclean v1.3.12. (https://bitbucket.org/izhbannikov/seqyclean/get/stable.zip) the quality filtering was performed. in order to generate the mapping file, accepted reads were mapped with tophat […]

[…] funcional aplicado a agropecuária e agroenergia at the university of são paulo using a hiscansq sequencer (illumina, san diego, ca)., 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 […]

[…] 0.10.1) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). all reads were filtered for phred quality (qs) 23 (sequence inside) and 30 (sequence edges) and minimum length of 65 bp using the seqyclean software (v.1.9.9) (https://github.com/ibest/seqyclean). the same package was also used to remove contaminant sequences (primers and vectors) using the univec database […]

[…] we also thank the center of functional genomics applied to agriculture and agroenergy (usp, campus “luiz de queiroz”) for generating the illumina miseq data., https://bitbucket.org/izhbannikov/seqyclean , the supplementary material for this article can be found online at: […]

[…] 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 […]

[…] to assembly, reads from all replicates were merged into a single dataset and the resulting fastq files (illumina) were filtered to remove low-quality bases (score < 30) and adapters, using the seqyclean pipeline (https://github.com/ibest/seqyclean). the remaining data were normalized by a single-pass digital normalization using the “normalize_by_kmer_coverage” procedure of the trinity […]

[…] 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) […]