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This tutorial explains how to get an API key from BaseSpace that you can use to automatically import your sequencing runs into Latch.

BaseSpace Downloader

Latch Bio

Latch is a platform for you to store, analyze, and visualize multiomics data

Getting Started on Latch

Latch Data is a cloud based file storage system built for storing biological data.

Overview

Basic Uploading and Downloading

Latch allows you to mount your own AWS S3 Buckets and use them the same as you would any data on Latch. All you need is to connect AWS account with Latch which will allow you to mount any buckets in that account onto Latch.

Mounting s3 Buckets

Command Line Interface

Data Sharing

FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.

FastQC

The Integrative Genomics Viewer (IGV) is a high-performance, easy-to-use, interactive tool for the visual exploration of genomic data. BAM, Fasta, etc. files can be opened in an IGV Browser natively within the Latch Platform. 

Using IGV on Latch

Learn how to set default viewer settings when opening files in IGV on Latch

Setting Viewer Defaults for IGV on Latch

The IGV browser comes with many hosted options for common Reference Genomes to view Alignment Files to. Here is a list of the options provided.

IGV Hosted Reference Genomes

All your sample sheets, all your metadata, all your analysis — in one place

Latch Registry

A project is a collection of tables. Let’s explore a few examples of how projects can be used:

Create a Project

What is a Project?

A table is a collection of records. Each record, also known as a row, contains a unique record name and a set of attributes.

Create a Table

Manually Create Single Records

Bulk Import Data Using a CSV

Bulk Link Sequencing Files to Existing Records

Modify Records in a Table

As you centralize your biological data in Latch Registry, you will often find that some records are related or even dependent on one another. Linked records offer a powerful way for you to define relationships between records from different tables, enhancing your data analysis and enabling new insights that may have been difficult to discover without linked records.

Connect Records Across Tables

Import Registry Records in Latch SDK Workflows

Latch Workflows come with out-of-the-box community workflows and a Python SDK that allows uploading of custom workflows.

Bulk RNA Seq

End-to-end bulk RNA-seq analysis using LVBRS

Every workflow in Latch allows you to import a CSV containing values for its parameters. This is another way to import data when doing bulk runs of a workflow.

CSV Import

In this tutorial, we will walk through the basics of creating your first Pod.

Latch Pod Basics

Best Practices for Working with Latch Data inside Pods

Mount the file system on Latch Data onto Pods

Mount Latch Data

You may want to set up SSH access for Pod if you want to access Pod from your local terminal or open your favorite IDE, such as Visual Studio Code, inside a Pod.

Set up SSH Access

Latch Pods make it easy to host any custom application, such as Dash Apps, RShiny, Streamlit, and more, on Latch.

Host a Custom App

Pods allow easy customization of auto shutdown interval when inactive.

Customize Auto Shutdown

Configure Pods for scheduled shutdown using systemd

Scheduled Shutdown

It is easy to use Visual Studio Code inside your Pod and navigate the filesystem on your favorite IDE.

Integration with VSCode

If you want to add a GitHub repository to Pod when Pod is created for the first time or commit to a GitHub repository in the future, you have to first set up your GitHub personal access token (PAT).

Integration with GitHub

Frequently Asked Questions

If there are any questions about privacy, please email privacy@latch.bio. We keep your name, email and company so you can use our system. We place cookies on your browser to make our system faster. We may use your name and email to send you information about our system. You are responsible for maintaining the privacy of data you enter into our system. We keep your data very private on our cloud providers. We follow the laws of all the countries where we operate. We follow the laws of Europe, like GDPR. If you need more information, see the sections below.

Introduction

Data

Visualizations

Registry

Workflows

Workflow Helpers

Pods

Resources