Portable genotype-free demultiplexing benchmarkign pipeline.

A portable pipeline for benchmarking genotype-free single-cell demultiplexing methods on simulated data.

The pipeline is designed to be generelisable to different datasets with arbitrary numbers of simulated mulitplexed samples. All software as part of pipeline is run through apptainer containers to ensure reproducibility and ease of use. The pipeline is designed to be run on a cluster with a slurm scheduler, but can be run locally ...

EC-Earth3 workflow with wrappers running in MeluXina with Autosubmit 3, used to assess the effects of task aggregation on queueing times. Workflow configuration is based on the Auto-EC-Earth3's testing suite [1].

In order to reduce the size of the workflow, the /proj and /tmp directories have been deleted. Additionally, the experiment has been cleaned up with the Autosubmit cleanup command. Authorized users will be able to fetch the project files from the original remote source.

[1] Garcia Lopez, ...

EC-Earth3 workflow with wrappers running in MeluXina with Autosubmit 3, used to assess the effects of task aggregation on queueing times. Workflow configuration is based on the Auto-EC-Earth3's testing suite [1].

In order to reduce the size of the workflow, the /proj and /tmp directories have been deleted. Additionally, the experiment has been cleaned up with the Autosubmit cleanup command. Authorized users will be able to fetch the project files from the original remote source.

[1] Garcia Lopez, ...

EC-Earth3 workflow with wrappers running in MareNostrum 5 with Autosubmit 3, used to assess the effects of task aggregation on queueing times. Workflow configuration is based on the Auto-EC-Earth3's testing suite [1].

In order to reduce the size of the workflow, the /proj and /tmp directories have been deleted. Additionally, the experiment has been cleaned up with the Autosubmit cleanup command. Authorized users will be able to fetch the project files from the original remote source.

[1] Garcia ...

EC-Earth3 workflow with wrappers running in MareNostrum 5 with Autosubmit 3, used to assess the effects of task aggregation on queueing times. Workflow configuration is based on the Auto-EC-Earth3's testing suite [1].

In order to reduce the size of the workflow, the /proj and /tmp directories have been deleted. Additionally, the experiment has been cleaned up with the Autosubmit cleanup command. Authorized users will be able to fetch the project files from the original remote source.

[1] Garcia ...

EC-Earth3 workflow with wrappers running in MareNostrum 4 with Autosubmit 3, used to assess the effects of task aggregation on queueing times. Workflow configuration is based on the Auto-EC-Earth3's testing suite [1].

In order to reduce the size of the workflow, the /proj and /tmp directories have been deleted. Additionally, the experiment has been cleaned up with the Autosubmit cleanup command. Authorized users will be able to fetch the project files from the original remote source.

[1] Garcia ...

EC-Earth3 workflow with wrappers running in MareNostrum 4 with Autosubmit 3, used to assess the effects of task aggregation on queueing times. Workflow configuration is based on the Auto-EC-Earth3's testing suite [1].

In order to reduce the size of the workflow, the /proj and /tmp directories have been deleted. Additionally, the experiment has been cleaned up with the Autosubmit cleanup command. Authorized users will be able to fetch the project files from the original remote source.

[1] Garcia ...

This workflow extracts protein-coding sequences from whole genome sequencing (WGS) data obtained from the European Nucleotide Archive (ENA). It automates the preprocessing, annotation, and selection of relevant protein sequences using tools such as Prokka, FASTA-to-Tabular, and pattern-based selection. The resulting dataset supports downstream analyses including comparative genomics, phylogenetics, and functional annotation.

GenErode pipeline

GitHub repository for GenErode, a Snakemake workflow for the analysis of whole-genome sequencing data from historical and modern samples to study patterns of genome erosion.

Documentation

The full pipeline documentation can be found on the repository wiki.

Citation

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Automated image processing from movies to 3D reconstruction. Includes CTF estimation, quality filters, box size estimation, picking model training, three 2D classification jobs (25k, 50k, and 100k particles), and 3D processing of the first 200k particles. Multiple 3D models are generated without symmetry, with automatic 2D and 3D class selection, using Relion.