#fastq — Public Fediverse posts

Pipeline release! nf-core/viralmetagenome v1.1.1 - v1.1.1 - Azure Albatross!
A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
Please see the changelog: https://github.com/nf-core/viralmetagenome/releases/tag/1.1.1

#epidemiology #fastq #ngs #viralmetagenomics #virology #virusgenomes #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/viralmetagenome v1.1.1 - v1.1.1 - Azure Albatross!
A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
Please see the changelog: https://github.com/nf-core/viralmetagenome/releases/tag/1.1.1

#epidemiology #fastq #ngs #viralmetagenomics #virology #virusgenomes #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/viralmetagenome v1.1.1 - v1.1.1 - Azure Albatross!
A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
Please see the changelog: https://github.com/nf-core/viralmetagenome/releases/tag/1.1.1

#epidemiology #fastq #ngs #viralmetagenomics #virology #virusgenomes #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/viralmetagenome v1.1.1 - v1.1.1 - Azure Albatross!
A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
Please see the changelog: https://github.com/nf-core/viralmetagenome/releases/tag/1.1.1

#epidemiology #fastq #ngs #viralmetagenomics #virology #virusgenomes #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/viralmetagenome v1.1.1 - v1.1.1 - Azure Albatross!
A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
Please see the changelog: https://github.com/nf-core/viralmetagenome/releases/tag/1.1.1

#epidemiology #fastq #ngs #viralmetagenomics #virology #virusgenomes #nfcore #openscience #nextflow #bioinformatics

Matthias Bethge (Tübingen University) proposes #OpenPipeline – inspired by open scientific data formats like #fastq - for more meaningful empirical comparison across LLM training systems #OpenSourceLLM

Matthias Bethge (Tübingen University) proposes #OpenPipeline – inspired by open scientific data formats like #fastq - for more meaningful empirical comparison across LLM training systems #OpenSourceLLM

Matthias Bethge (Tübingen University) proposes #OpenPipeline – inspired by open scientific data formats like #fastq - for more meaningful empirical comparison across LLM training systems #OpenSourceLLM

Matthias Bethge (Tübingen University) proposes #OpenPipeline – inspired by open scientific data formats like #fastq - for more meaningful empirical comparison across LLM training systems #OpenSourceLLM

Matthias Bethge (Tübingen University) proposes #OpenPipeline – inspired by open scientific data formats like #fastq - for more meaningful empirical comparison across LLM training systems #OpenSourceLLM

Pipeline release! nf-core/viralmetagenome v1.1.0 - v1.1.0 - Virid Hen!
A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
Please see the changelog: https://github.com/nf-core/viralmetagenome/releases/tag/1.1.0

#epidemiology #fastq #ngs #viralmetagenomics #virology #virusgenomes #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/viralmetagenome v1.1.0 - v1.1.0 - Virid Hen!
A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
Please see the changelog: https://github.com/nf-core/viralmetagenome/releases/tag/1.1.0

#epidemiology #fastq #ngs #viralmetagenomics #virology #virusgenomes #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/viralmetagenome v1.1.0 - v1.1.0 - Virid Hen!
A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
Please see the changelog: https://github.com/nf-core/viralmetagenome/releases/tag/1.1.0

#epidemiology #fastq #ngs #viralmetagenomics #virology #virusgenomes #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/viralmetagenome v1.1.0 - v1.1.0 - Virid Hen!
A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
Please see the changelog: https://github.com/nf-core/viralmetagenome/releases/tag/1.1.0

#epidemiology #fastq #ngs #viralmetagenomics #virology #virusgenomes #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/viralmetagenome v1.1.0 - v1.1.0 - Virid Hen!
A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
Please see the changelog: https://github.com/nf-core/viralmetagenome/releases/tag/1.1.0

#epidemiology #fastq #ngs #viralmetagenomics #virology #virusgenomes #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/viralmetagenome v1.0.1 - 1.0.1 - Khaki Quail!
A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
Please see the changelog: https://github.com/nf-core/viralmetagenome/releases/tag/1.0.1

#epidemiology #fastq #ngs #viralmetagenomics #virology #virusgenomes #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/viralmetagenome v1.0.1 - 1.0.1 - Khaki Quail!
A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
Please see the changelog: https://github.com/nf-core/viralmetagenome/releases/tag/1.0.1

#epidemiology #fastq #ngs #viralmetagenomics #virology #virusgenomes #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/viralmetagenome v1.0.1 - 1.0.1 - Khaki Quail!
A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
Please see the changelog: https://github.com/nf-core/viralmetagenome/releases/tag/1.0.1

#epidemiology #fastq #ngs #viralmetagenomics #virology #virusgenomes #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/viralmetagenome v1.0.1 - 1.0.1 - Khaki Quail!
A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
Please see the changelog: https://github.com/nf-core/viralmetagenome/releases/tag/1.0.1

#epidemiology #fastq #ngs #viralmetagenomics #virology #virusgenomes #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/viralmetagenome v1.0.1 - 1.0.1 - Khaki Quail!
A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
Please see the changelog: https://github.com/nf-core/viralmetagenome/releases/tag/1.0.1

#epidemiology #fastq #ngs #viralmetagenomics #virology #virusgenomes #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/detaxizer v1.2.0 - detaxizer 1.2.0 - Kunschd!

Please see the changelog: https://github.com/nf-core/detaxizer/releases/tag/1.2.0

#deidentification #decontamination #edna #fastq #filter #longreads #metabarcoding #metagenomics #microbiome #nanopore #shortreads #shotgun #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/detaxizer v1.2.0 - detaxizer 1.2.0 - Kunschd!

Please see the changelog: https://github.com/nf-core/detaxizer/releases/tag/1.2.0

#deidentification #decontamination #edna #fastq #filter #longreads #metabarcoding #metagenomics #microbiome #nanopore #shortreads #shotgun #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/detaxizer v1.2.0 - detaxizer 1.2.0 - Kunschd!

Please see the changelog: https://github.com/nf-core/detaxizer/releases/tag/1.2.0

#deidentification #decontamination #edna #fastq #filter #longreads #metabarcoding #metagenomics #microbiome #nanopore #shortreads #shotgun #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/detaxizer v1.2.0 - detaxizer 1.2.0 - Kunschd!

Please see the changelog: https://github.com/nf-core/detaxizer/releases/tag/1.2.0

#deidentification #decontamination #edna #fastq #filter #longreads #metabarcoding #metagenomics #microbiome #nanopore #shortreads #shotgun #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/detaxizer v1.2.0 - detaxizer 1.2.0 - Kunschd!

Please see the changelog: https://github.com/nf-core/detaxizer/releases/tag/1.2.0

#deidentification #decontamination #edna #fastq #filter #longreads #metabarcoding #metagenomics #microbiome #nanopore #shortreads #shotgun #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/fastqrepair v1.0.0 - nf-core/fastqrepair v1.0.0 - Catanzaro YellowRed!

Please see the changelog: https://github.com/nf-core/fastqrepair/releases/tag/1.0.0

#corruption #datacleaning #datarecovery #fastq #fastqcorrupted #fastqformat #readsinterleaving #recoverytool #unpairedreads #wellformed #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/fastqrepair v1.0.0 - nf-core/fastqrepair v1.0.0 - Catanzaro YellowRed!

Please see the changelog: https://github.com/nf-core/fastqrepair/releases/tag/1.0.0

#corruption #datacleaning #datarecovery #fastq #fastqcorrupted #fastqformat #readsinterleaving #recoverytool #unpairedreads #wellformed #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/fastqrepair v1.0.0 - nf-core/fastqrepair v1.0.0 - Catanzaro YellowRed!

Please see the changelog: https://github.com/nf-core/fastqrepair/releases/tag/1.0.0

#corruption #datacleaning #datarecovery #fastq #fastqcorrupted #fastqformat #readsinterleaving #recoverytool #unpairedreads #wellformed #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/fastqrepair v1.0.0 - nf-core/fastqrepair v1.0.0 - Catanzaro YellowRed!

Please see the changelog: https://github.com/nf-core/fastqrepair/releases/tag/1.0.0

#corruption #datacleaning #datarecovery #fastq #fastqcorrupted #fastqformat #readsinterleaving #recoverytool #unpairedreads #wellformed #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/fastqrepair v1.0.0 - nf-core/fastqrepair v1.0.0 - Catanzaro YellowRed!

Please see the changelog: https://github.com/nf-core/fastqrepair/releases/tag/1.0.0

#corruption #datacleaning #datarecovery #fastq #fastqcorrupted #fastqformat #readsinterleaving #recoverytool #unpairedreads #wellformed #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/detaxizer v1.1.0 - detaxizer 1.1.0 - Kombjuudr!

Please see the changelog: https://github.com/nf-core/detaxizer/releases/tag/1.1.0

#deidentification #decontamination #edna #fastq #filter #longreads #metabarcoding #metagenomics #microbiome #nanopore #shortreads #shotgun #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/detaxizer v1.1.0 - detaxizer 1.1.0 - Kombjuudr!

Please see the changelog: https://github.com/nf-core/detaxizer/releases/tag/1.1.0

#deidentification #decontamination #edna #fastq #filter #longreads #metabarcoding #metagenomics #microbiome #nanopore #shortreads #shotgun #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/detaxizer v1.1.0 - detaxizer 1.1.0 - Kombjuudr!

Please see the changelog: https://github.com/nf-core/detaxizer/releases/tag/1.1.0

#deidentification #decontamination #edna #fastq #filter #longreads #metabarcoding #metagenomics #microbiome #nanopore #shortreads #shotgun #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/detaxizer v1.1.0 - detaxizer 1.1.0 - Kombjuudr!

Please see the changelog: https://github.com/nf-core/detaxizer/releases/tag/1.1.0

#deidentification #decontamination #edna #fastq #filter #longreads #metabarcoding #metagenomics #microbiome #nanopore #shortreads #shotgun #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/detaxizer v1.1.0 - detaxizer 1.1.0 - Kombjuudr!

Please see the changelog: https://github.com/nf-core/detaxizer/releases/tag/1.1.0

#deidentification #decontamination #edna #fastq #filter #longreads #metabarcoding #metagenomics #microbiome #nanopore #shortreads #shotgun #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

@CjrrEvol I've been toying with #rust #rustlang when I make #cli tools that help me with common tasks. For example, when inspecting the flow cell and sequencing info in #FASTQ files, I use this:

https://gitlab.com/jrhawley/bio-jtools

I think Rust is great and I really wish I could use it more often. But I think there are a few barriers for people using Rust in #bioinformatics more often.

I've been submitting single #HPC jobs that loop over long lists of #fastq sequence files in my #GBS pipeline. Using this approach, my current project was going to take 50+ days to get through just #ustacks.

Just figured out how to use #slurm job arrays, and it looks like I'll be done inside 24 hours!

I'm on holiday in Japan, and with time to kill during the day, I managed a small blog post:

https://blastedbio.blogspot.com/2024/06/fastq-uploads-to-ena-ftp-site-with.html

Abstract: I liked #rclone for uploading lots of #FASTQ files to the ENA FTP site, like bulk curl upload but with no-clobber support.

asked #biostars "htslib/c what is the correct way to use bgzf_thread_pool ?" #C #samtools #htskib #fastq https://www.biostars.org/p/9551841/

asked #biostars "htslib/c what is the correct way to use bgzf_thread_pool ?" #C #samtools #htskib #fastq https://www.biostars.org/p/9551841/

asked #biostars "htslib/c what is the correct way to use bgzf_thread_pool ?" #C #samtools #htskib #fastq https://www.biostars.org/p/9551841/

asked #biostars "htslib/c what is the correct way to use bgzf_thread_pool ?" #C #samtools #htskib #fastq https://www.biostars.org/p/9551841/

asked #biostars "htslib/c what is the correct way to use bgzf_thread_pool ?" #C #samtools #htskib #fastq https://www.biostars.org/p/9551841/

Thanked the contributors who authored a new tutorial to a project I helped maintain in a field that I would never imagine myself getting into without my head spinning. #genomics #FASTQ

RE: https://bsky.app/profile/did:plc:wb4chyxecnojex7l6vyha2xf/post/3lbdtw4fme22m