A bioinformatics pipeline for whole exome sequencing: overview of the processing and steps from raw data to downstream analysis
… 50% threshold) and the nucleotide distribution across all reads. In our pipeline, we used
FastQC (with default Phred = 20 value) as it plots the read depth and quality score besides a …
FastQC (with default Phred = 20 value) as it plots the read depth and quality score besides a …
[HTML][HTML] SECAPR—a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments
… Capture Processor (SECAPR) pipeline for processing raw sequencing data into multiple
sequence … SECAPR is an easy-to-use, free, and versatile pipeline, aimed to enable efficient and …
sequence … SECAPR is an easy-to-use, free, and versatile pipeline, aimed to enable efficient and …
[HTML][HTML] TreeToReads-a pipeline for simulating raw reads from phylogenies
EJ McTavish, J Pettengill, S Davis, H Rand, E Strain… - … bioinformatics, 2017 - Springer
… To resolve this problem, we offer a program, TreeToReads, which can generate raw read
data from mutated genomes simulated under a known phylogeny. This simulation pipeline …
data from mutated genomes simulated under a known phylogeny. This simulation pipeline …
SNAPR: a bioinformatics pipeline for efficient and accurate RNA-seq alignment and analysis
… read counts internally, while read counts for STAR and Tophat2/Bowtie2 were generated
using htseqcount. Computed gene read counts were compared to the exact gene read … the raw …
using htseqcount. Computed gene read counts were compared to the exact gene read … the raw …
[HTML][HTML] A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome
I Allali, JW Arnold, J Roach, MB Cadenas, N Butz… - BMC microbiology, 2017 - Springer
… The GS FLX+ run produced the lowest number of raw reads (1/8 of a plate) compared to
PGM (314X chip) and MiSeq (one lane); however, quality scores were higher in comparison to …
PGM (314X chip) and MiSeq (one lane); however, quality scores were higher in comparison to …
pipeliner: Software to evaluate the performance of bioinformatics pipelines for next‐generation resequencing
B Nevado, M Perez‐Enciso - Molecular ecology resources, 2015 - Wiley Online Library
… (s) with the raw NGS reads. … pipelines, thus allowing the use of any software package(s) to
simulate the original sequence data and the NGS short reads, or to perform the bioinformatics …
simulate the original sequence data and the NGS short reads, or to perform the bioinformatics …
[HTML][HTML] Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines
N Kulkarni, L Alessandrì, R Panero, M Arigoni… - … bioinformatics, 2018 - Springer
… a complex bioinformatics analysis, the raw data and the list … regions and to merge overlapping
reads. We have also … ], to discriminate between human reads and mouse host reads in the …
reads. We have also … ], to discriminate between human reads and mouse host reads in the …
[HTML][HTML] Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing
A Prodan, V Tremaroli, H Brolin, AH Zwinderman… - PLoS …, 2020 - journals.plos.org
… pipelines and there is a lack of agreement regarding best practices. Here, we compared six
bioinformatic pipelines … Raw reads were imported into a Qiime2 artifact before merging paired…
bioinformatic pipelines … Raw reads were imported into a Qiime2 artifact before merging paired…
A simplest bioinformatics pipeline for whole transcriptome sequencing: Overview of the processing and steps from raw data to downstream analysis
… studies rely on the raw data as it delivers a prompt insight of the sequence quality for further
downstream analysis. In our pipeline, we used FastQC as it plots the read depth and quality …
downstream analysis. In our pipeline, we used FastQC as it plots the read depth and quality …
[HTML][HTML] Standards and guidelines for validating next-generation sequencing bioinformatics pipelines: a joint recommendation of the Association for Molecular …
… For each nucleotide sequenced in these short fragments (ie, raw reads), a corresponding
Phred-like quality score is assigned, which is sequencing platform specific. The read …
Phred-like quality score is assigned, which is sequencing platform specific. The read …
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