Charles Hefer
@charleshefer.bsky.social
Bioinformatics scientist / genomics / transcriptomics / proteomics. Spends days playing with R, Python and workflow systems, trying to solve interesting problems. Living in Aotearoa, and exploring all over. 🇳🇿🇿🇦
Reposted by Charles Hefer
🦠🧬💻 Bakta v1.10 - largest update so far:
Highlights:
- user-provided HMMs: --hmms
- output file recovery from JSON files: bakta_io
- export of inference metrics: inference.tsv
- bypass overlap filters: --skip-filter
- improved genome plots
github.com/oschwengers/...
👇 (1/11)
Highlights:
- user-provided HMMs: --hmms
- output file recovery from JSON files: bakta_io
- export of inference metrics: inference.tsv
- bypass overlap filters: --skip-filter
- improved genome plots
github.com/oschwengers/...
👇 (1/11)
Release v1.10 - Novel in & novel out · oschwengers/bakta
This is the tenth minor release (v1.10) introducing user-provided HMMs, output file recovery, feature inference scores, and various improvements.
Compatible database scheme version: 5
Important
Si...
github.com
November 18, 2024 at 8:49 AM
🦠🧬💻 Bakta v1.10 - largest update so far:
Highlights:
- user-provided HMMs: --hmms
- output file recovery from JSON files: bakta_io
- export of inference metrics: inference.tsv
- bypass overlap filters: --skip-filter
- improved genome plots
github.com/oschwengers/...
👇 (1/11)
Highlights:
- user-provided HMMs: --hmms
- output file recovery from JSON files: bakta_io
- export of inference metrics: inference.tsv
- bypass overlap filters: --skip-filter
- improved genome plots
github.com/oschwengers/...
👇 (1/11)
Reposted by Charles Hefer
🚀 New Helixer tutorial for gene prediction! Predict genes in complex genomes like maize with 1 command—no repeatmasking, no extra data needed, all under 4 hrs! 🌽💻
Check it out: rcac-bioinformatics.readthedocs.io/en/latest/he...
#Bioinformatics #Genomics #RCAC
Check it out: rcac-bioinformatics.readthedocs.io/en/latest/he...
#Bioinformatics #Genomics #RCAC
Gene prediction using Helixer — RCAC bioinformatics tutorials
rcac-bioinformatics.readthedocs.io
October 31, 2024 at 2:42 PM
🚀 New Helixer tutorial for gene prediction! Predict genes in complex genomes like maize with 1 command—no repeatmasking, no extra data needed, all under 4 hrs! 🌽💻
Check it out: rcac-bioinformatics.readthedocs.io/en/latest/he...
#Bioinformatics #Genomics #RCAC
Check it out: rcac-bioinformatics.readthedocs.io/en/latest/he...
#Bioinformatics #Genomics #RCAC
Reposted by Charles Hefer
🧵 Bioinformatics faces a critical challenge: despite its importance, software quality often falls short due to the lack of proper development practices.
In our latest paper, we advocate for improving software quality in bioinformatics through teamwork.
academic.oup.com/bioinformati...
In our latest paper, we advocate for improving software quality in bioinformatics through teamwork.
academic.oup.com/bioinformati...
November 18, 2024 at 2:48 PM
🧵 Bioinformatics faces a critical challenge: despite its importance, software quality often falls short due to the lack of proper development practices.
In our latest paper, we advocate for improving software quality in bioinformatics through teamwork.
academic.oup.com/bioinformati...
In our latest paper, we advocate for improving software quality in bioinformatics through teamwork.
academic.oup.com/bioinformati...
Reposted by Charles Hefer
Cluster-efficient pangenome graph construction with nf-core/pangenome https://academic.oup.com/bioinformatics/article/40/11/btae609/7821182 🧬🖥️🧪 https://github.com/nf-core/pangenome
November 16, 2024 at 4:44 PM
Cluster-efficient pangenome graph construction with nf-core/pangenome https://academic.oup.com/bioinformatics/article/40/11/btae609/7821182 🧬🖥️🧪 https://github.com/nf-core/pangenome