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GIPhy / AlienDiscover · GitLab Inferring alien oligonucleotides (adapter, primer, index, barcode, ...) without any prior or external knowledge

AlienDiscover: 🆕 v0.3 available to infer alien oligos (adapter, index, barcode, heteropolymer, ...) from #FASTQ files

✅ new confidence score for each inferred #long-read alien oligos
✅ ability to filter out #long-read alien oligos with low score
✅ still fast

gitlab.pasteur.fr/GIPhy/AlienDiscover

GIPhy / ASSU · GitLab Assembling SSU

ASSU: 🆕 version 1.2 for quickly ASSembling SSU (16S) rRNA segments using short HTS reads derived from prokaryote WGS.
#bioinformatics #FASTQ #16S #rRNA

➡️ new preset options for better sensitivity 🧬
➡️ up-to-date SSU reference databank 🦠

gitlab.pasteur.fr/GIPhy/ASSU
research.pasteur.fr/en/tool/assu

fastp 1.0: An ultra‐fast all‐round tool for FASTQ data quality control and preprocessing The figure shows side-by-side quality comparison of the data before and after preprocessing using fastp 1.0. As can be seen from this figure, the data quality has been significantly improved after fa...

🚀 #fastp: ultra-fast, full-featured & user-friendly #FASTQ preprocessing tool!
☁️ Cloud-friendly, minimal resources, web-based reports
📊 v1.0 brings enhanced HTML reporting & parallel batch processing
onlinelibrary.wiley.com/doi/10.1002/...
#Bioinformatics #NGS #sequencing

All you need is:
1) Transcriptome (equivalent of transcriptome #FASTA file)
2) Gene annotations (equivalent of #GTF/#GFF file)
3) RNAseq reads (your #FASTQ file)

#BgeeCall will handle the rest and will let you know if a gene is present or absent!

FQsum performances

FQsum: high-speed estimate of a full range of descriptive statistics from #FASTQ files
#bioinformatics #short-reads #long-reads

gitlab.pasteur.fr/GIPhy/FQsum

GIPhy / AlienDiscover · GitLab Inferring alien oligonucleotides (adapters, primers, ...) from FASTQ file

AlienDiscover: 🆕 version 0.2 available

inference of alien oligonucleotides (adapter, primer, index, barcode, ...) without any prior nor external knowledge

➡️ still accurate on #short-read #FASTQ files
➡️ now able to deal with #long-read #FASTQ files
➡️ very fast

gitlab.pasteur.fr/GIPhy/AlienDiscover

GIPhy / AlienTrimmer · GitLab Fast trimming of sequencing reads

AlienTrimmer: 🆕 version 3.0 available
@sylvainbrisse.bsky.social @pasteur.fr

☑️ now able to clip low-residue content regions
☑️ deal with Phred scores up to 95
☑️ still one of the fastest #FASTQ clipping/trimming tool

gitlab.pasteur.fr/GIPhy/AlienTrimmer
research.pasteur.fr/en/software/alientrimmer

Véronique LEGRAND / ROCK · GitLab Institut Pasteur Gitlab

ROCK (Reducing Over-Covering K-mers): 🆕 version 3.0
#bioinformatics #FASTQ #LongReads

➡️ now able to quickly perform digital normalization on long-read data files

gitlab.pasteur.fr/vlegrand/ROCK
research.pasteur.fr/en/software/rock

wgetENAHTS

wgetENAHTS: 🆕 version 4.3

multi-threaded #FASTQ file downloading from the European Nucleotide Archive (ENA) repository

➡️ now deals with the last ENA file report format

gitlab.pasteur.fr/GIPhy/wgetENAHTS

fq2dna (FASTQ 2 de novo assembly)

fq2dna: 🆕 version 25.03
#genomics #FASTQ #bioinformatics

✔️ new accuracy index
✔️ compatible with up-to-date dependency versions
✔️ several bugs fixed

gitlab.pasteur.fr/GIPhy/fq2dna
research.pasteur.fr/en/tool/fq2dna

fqCleanER (fastq Cleaning and Enhancing Routine)

fqCleanER: 🆕 version 25.03
#bioinformatics #FASTQ

➡️ updated list of alien oligos
➡️ updated trap and TMPDIR handling
➡️ several fixed minor bugs

gitlab.pasteur.fr/GIPhy/fqCleanER
research.pasteur.fr/en/tool/fqcleaner

Véronique LEGRAND / ROCK · GitLab Institut Pasteur Gitlab

ROCK (Reducing Over-Covering K-mers): new version 2.1
#bioinformatics #FASTQ

=> fixed bug that (rarely) occurs when processing very large FASTQ files

gitlab.pasteur.fr/vlegrand/ROCK
research.pasteur.fr/en/software/rock

JARVIS3: an efficient encoder for genomic data AbstractMotivation. Large-scale genomic projects grapple with the complex challenge of reducing medium- and long-term storage space and its associated ener

JARVIS3: an efficient encoder for genomic data. #SequencingData #Fasta #Fastq #ReferenceFreeCompression #LosslessCompression #GenomicsData #Bioinformatics 🧬 🖥️
Github: github.com/cobilab/jarv...

academic.oup.com/bioinformati...

GitHub - lskatz/fasten: :construction_worker: Fasten toolkit, for streaming operations on fastq file... :construction_worker: Fasten toolkit, for streaming operations on fastq files - GitHub - lskatz/fasten: :construction_worker: Fasten toolkit, for streaming operations on fastq files

Exciting news! 🚀 Just released two powerful tools for #FastQ analysis in my Fasten repo at github.com/lskatz/fasten

Give them a try and supercharge your #bioinformatics workflow.

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

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