Review




Structured Review

Oxford Nanopore raw sequencing output
Sphae workflow overview. The workflow processes <t>sequencing</t> reads from short- and/or long-read data in fastq format. The command sphae run, starts with quality control, filtering out low-quality reads and adaptor sequences. Processed reads are assembled, and the resulting assemblies are processed to confirm complete phage genomes in each sample. The phage genomes are annotated to identify the genes and assign biological functions. The final output folder contains the assembled genome (fasta format), annotations (GenBank format), a Circos plot (PNG format), and a summary text file detailing phage characteristics.
Raw Sequencing Output, supplied by Oxford Nanopore, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/raw+sequencing+data+processing/raw+sequencing+data/pmc11783317-85-2-0
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raw sequencing output - by Bioz Stars, 2026-09
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1) Product Images from "Sphae: an automated toolkit for predicting phage therapy candidates from sequencing data"

Article Title: Sphae: an automated toolkit for predicting phage therapy candidates from sequencing data

Journal: Bioinformatics Advances

doi: 10.1093/bioadv/vbaf004

Sphae workflow overview. The workflow processes sequencing reads from short- and/or long-read data in fastq format. The command sphae run, starts with quality control, filtering out low-quality reads and adaptor sequences. Processed reads are assembled, and the resulting assemblies are processed to confirm complete phage genomes in each sample. The phage genomes are annotated to identify the genes and assign biological functions. The final output folder contains the assembled genome (fasta format), annotations (GenBank format), a Circos plot (PNG format), and a summary text file detailing phage characteristics.
Figure Legend Snippet: Sphae workflow overview. The workflow processes sequencing reads from short- and/or long-read data in fastq format. The command sphae run, starts with quality control, filtering out low-quality reads and adaptor sequences. Processed reads are assembled, and the resulting assemblies are processed to confirm complete phage genomes in each sample. The phage genomes are annotated to identify the genes and assign biological functions. The final output folder contains the assembled genome (fasta format), annotations (GenBank format), a Circos plot (PNG format), and a summary text file detailing phage characteristics.

Techniques Used: Sequencing, Control

Related Articles

Generated:

Article Title: Efficient targeted recombination with CRISPR/Cas9 in hybrids of Caenorhabditis nematodes with suppressed recombination
Article Snippet: .. The Oxford Nanopore sequencing raw reads generated in this study were submitted to the NCBI BioProject database under accession number PRJNA947947. ..

Sequencing:

Article Title: Comparative genomic analysis identifies potential adaptive variation in Mycoplasma ovipneumoniae
Article Snippet: .. For samples with ONT sequence data, raw ONT sequence reads were demultiplexed by barcode and base-called using Guppy v.4.2.2 (Oxford Nanopore Technologies Ltd.). ..

Article Title: Phage therapy candidates from Sphae: An automated toolkit for predicting sequencing data
Article Snippet: Sphae requires sequencing reads in fastq format, either paired-end short reads from Illumina or MGI sequencing platforms or unpaired long reads from Oxford Nanopore sequencing platforms. .. Oxford Nanopore raw sequencing output is in fast5 or pod5 format, which must be basecalled using Guppy ( https://community.nanoporetech.com ) or Dorado ( https://github.com/nanoporetech/dorado ) to convert the reads to fastq format before running this workflow. ..

Article Title: Hecatomb: an integrated software platform for viral metagenomics
Article Snippet: .. Hecatomb (RRID: SCR_025002) serves as an end-to-end pipeline by processing raw sequencing reads (single or paired end, long or short reads from Illumina, MGI, PacBio, or Oxford Nanopore platforms) through 4 key modules (Fig. ). ..

Article Title: Sphae: an automated toolkit for predicting phage therapy candidates from sequencing data
Article Snippet: Sphae requires sequencing reads in fastq format, either paired-end short reads from Illumina or MGI sequencing platforms or unpaired long reads from Oxford Nanopore sequencing platforms. .. Oxford Nanopore raw sequencing output is in fast5 or pod5 format, which must be basecalled using Guppy or Dorado to convert the reads to fastq format before running this workflow. ..

Article Title: Transcriptomics data for muscle development in Goats
Article Snippet: .. Quality control of Oxford Nanopore Technology (ONT) raw sequencing data was conducted based on sequencing quality scores, with a default threshold of Q7. ..

Article Title: The need for speed: ultra-rapid high-resolution outbreak analysis in a front-line hospital microbiology laboratory
Article Snippet: .. The Oxford Nanopore Technologies raw sequence read data, basecalled using Dorado v0.6.3, have been deposited in the National Center for Biotechnology Information (NCBI) sequence read archive (SRA, https://www.ncbi.nlm.nih.gov/sra ). ..

Control:

Article Title: Transcriptomics data for muscle development in Goats
Article Snippet: .. Quality control of Oxford Nanopore Technology (ONT) raw sequencing data was conducted based on sequencing quality scores, with a default threshold of Q7. ..



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Image Search Results


Top 15 biological pathways significantly enriched for the differentially expressed  mRNA  genes identified through  mRNA   sequencing  of the paired endometrioma–endometrium cohort.

Journal: Biomolecules

Article Title: miR-193b-5p and miR-374b-5p Are Aberrantly Expressed in Endometriosis and Suppress Endometrial Cell Migration In Vitro

doi: 10.3390/biom14111400

Figure Lengend Snippet: Top 15 biological pathways significantly enriched for the differentially expressed mRNA genes identified through mRNA sequencing of the paired endometrioma–endometrium cohort.

Article Snippet: Differentially expressed genes with an FDR < 0.05 and fold change of <−2 or >˃2 were considered significant. mRNA sequencing data analysis: the raw mRNA sequencing data processing and analysis were performed using the Partek ® Flow ® platform (version 10.0.22.1005).

Techniques: Sequencing, Infection, Virus