Show threado lаvrоvskyFeb 9
Matthias Bethge (Tübingen University) proposes #OpenPipeline – inspired by open scientific data formats like #fastq - for more meaningful empirical comparison across LLM training systems #OpenSourceLLM
nf-coreJan 23

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

nf-coreDec 5

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

nf-coreAug 7, 2025

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

Release detaxizer 1.2.0 - Kunschd · nf-core/detaxizer

Summary of changes filtering is set now by default defaults reflect best settings from benchmarking human decontamination improvements to memory and time requirements Detailed changes Added PR #...

GitHub
nf-coreFeb 3, 2025

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

Release nf-core/fastqrepair v1.0.0 - Catanzaro YellowRed · nf-core/fastqrepair

Initial release of nf-core/fastqrepair! 🎉 Updates of markdown files and default values in schema by @mazzalab in #1 Important! Template update for nf-core/tools v3.1.0 by @mazzalab in #10 Importan...

GitHub
Show threadYuan TangOct 30, 2021
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
Yuan TangFeb 12, 2020
A new tutorial for loading and preparing genomics data via @TensorFlow I/O is available in http://bit.ly/2SjsozB! Thanks @suyash_builds for spearheading this and @billylamberta @DaoustMj from TensorFlow docs team! #genomics #FASTQ
TensorFlow I/O

TensorFlow
nf-coreNov 8, 2024

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

Release detaxizer 1.1.0 - Kombjuudr · nf-core/detaxizer

Added PR #34 - Added bbduk to the classification step (kraken2 as default, both can be run together) (by @jannikseidelQBiC) PR #34 - Added --fasta_bbduk parameter to provide a fasta file with cont...

GitHub
Show threadJames Hawley, PhDOct 4, 2024

@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.

James Hawley / bio-jtools · GitLab

A suite of bioinformatics tools for interacting with high throughput sequencing (HTS) data, written entirely in Rust

GitLab
Tyler SmithJul 4, 2024

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!