galaxy
orfipy
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| galaxy | orfipy | |
|---|---|---|
| 4 | 2 | |
| 1,313 | 46 | |
| 2.6% | - | |
| 10.0 | 1.8 | |
| 5 days ago | over 2 years ago | |
| Python | Python | |
| GNU General Public License v3.0 or later | MIT License |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
galaxy
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Need for GUIs for bioinformatic tools?
Maybe it would help you to look at the galaxy project: GitHub main site
- BIOINFORMATICS PROJECT
- Any bioinfo open source projects looking for contributors?
- Developed a new kind of dual extruder system on fully custom built 3D printer
orfipy
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Looking for a tool to convert a whole fasta file with CDS sequences to a fasta file with protein sequences.
You can probably use or adapt https://github.com/urmi-21/orfipy. I've never used this but it looks fantastic.
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Question about ORF finder
You don't need any specific hardware to run most bioinformatics programs. There is a web application of ORF finder and if you want to run large amounts of analyses you probably want to run them in a Linux environment. Look at Windows Subsystem for Linux if you are a Windows user. You may also be interested in new ORF finders like this one: https://github.com/urmi-21/orfipy
What are some alternatives?
nextflow - A DSL for data-driven computational pipelines
Biopython - Official git repository for Biopython (originally converted from CVS)
pyrodigal - Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
deepvariant - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
reCOGnizer - A tool for domain based annotation with databases from the Conserved Domains Database
fastp - An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
sarek - Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
galaxy_ng - Ansible Galaxy Server - Issues on https://forum.ansible.com Docs on https://galaxy-ng.readthedocs.io/
ncbi-genome-download - Scripts to download genomes from the NCBI FTP servers
ansible-proxmox - Ansible for provisioning proxmox servers
goatools - Python library to handle Gene Ontology (GO) terms