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SBG Public Pipelines

Showing 34 pipelines.

Seven Bridges Public Pipelines are ready-to-run bioinformatic analysis workflows. We've strung together apps that take you from raw data file to processed file or interpretable result. Small utility pipelines like Merge FASTQ Files are comprised of single apps. Use them to perform simple tasks and learn how pipelines are constructed. Pipelines that are more complicated - Variant Calling from Single Samples - BWA + GATK for example - reproduce published analyses so that you can process your data like a pro.

Browse a few pipelines, read their descriptions and take a look at their parts. Find one that fits your needs, copy it to your project, then run it as is or modify it to suit your data. If you need something entirely new, no problem - you can build from scratch using Seven Bridges visual editor. And if you haven’t opened an account yet, go ahead. It’s free.

Amplicon Experiment QC

Allows you to do quick quality control of amplicon based targetted experiments by generating a heatmap of the coverage.

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Trio analysis pipeline (Whole Genome)

Whole genome trio analysis pipeline introduces custom analysis for detecting de novo mutations within trios using multiple callers to reduce the false positive rate

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FastQC Analysis

FastQC tool analyzes sequence read data from FASTQ, BAM, or SAM files and generate a set of reports.

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Alignment Metrics QC

Analyze the quality of read alignment for both genomic and transcriptomic experiments with this quality control pipeline.

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Exome Coverage QC

Assess the quality of your exome sequencing library preparation: calculate and visualize coverage statistics.

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Merge FASTQ Files

Merge multiple FASTQ files into a single FASTQ file. Useful when reads for a sample have been split over multiple files.

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Convert SAM/BAM to FASTQ

Convert SAM or BAM files to FASTQ files to enable data processing with pipelines that use the standardized FASTQ format.

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Trio analysis pipeline (Whole Exome)

Whole exome trio analysis pipeline introduces custom analysis for detecting de novo mutations within trios using multiple callers to reduce the false positive rate.

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