HTSlib-based tools like bcftools and samtools provide powerful capabilities for working with genomic data stored on remote servers. Whether your data is in AWS S3, accessible via FTP, or hosted on HTTPS endpoints, these tools allow you to efficiently query and subset remote files without downloading entire datasets. This guide covers authentication, remote file access patterns, and practical workflows.
Pixi is a fast, modern package management tool built on the conda ecosystem. Whether you're on a personal laptop or an HPC cluster, Pixi makes environment setup simple and reproducible. Here’s a primer on using Pixi. For a full workflow, see: Setting up single-cell RNA-seq analysis with Pixi as collaboration between RIVERXDATA and NGS101
Simply, I just want a web application. This is an all-in-one application similar to Google Drive, but more advanced. It allows me to select files and put them into a workflow obtained directly from GitHub. For example, rnaseq from nf-core. The web application allows me to run and monitor Nextflow jobs. Then, it puts the results back to Google Drive, where I can view the results. It is useful for sharing results with my team or external teams. I can develop pipelines independently. My data can be stored on the cloud for backup. It is a simple and standard procedure for bioinformatics analysis. But I have not found any solution that fits these requirements is EASY, FREE, OPEN-SOURCE
If you feel the same, RIVER may be your choice.