Genomics
Bulk Sequencing
Logo | Title | Description | Data inputs |
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STAR Generate Genome Index capsule | Generates necessary files to run STAR RNA alignment |
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STAR Alignment | RNA-Seq alignment. STAR addresses many of the challenges of RNA-seq data mapping by accounting for spliced alignments This means that RNA sequences can successfully align to the DNA genome. |
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Salmon Preparing Transcriptome Indices for Mapping-Based Mode | Generates necessary files to run Salmon RNA alignment from genome RNA transcript fasta file and genome DNA genome fasta file. |
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Salmon: mapping-based quantification | RNA-Seq quantification. Salmon specifically is designed for speed and is more geared towards quantification of transcripts specifically than precise read alignment. |
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BWA Generate Genome Index | Generates necessary files to run BWA DNA alignment from a DNA fasta file.Genome DNA fasta |
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BWA Mem | BWA is a software package for mapping sequences against a large reference genome, such as the human genome. |
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Bowtie2 Generate Genome Index | Generates necessary files to run Bowtie DNA alignment from a DNA fasta file. |
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Bowtie2 | Bowtie is a software package for mapping sequences against a large reference genome, such as the human genome. |
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Single Cell
Logo | Title | Description | Data Inputs |
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STAR-Solo Alignment | STAR-Solo analyzes droplet single cell RNA sequencing data for example, 10X Genomics Chromium System. It is intended to be a drop in replacement for CellRanger from 10X |
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RShiny Cell | ShinyCell is an R package that allows users to create interactive Shiny-based web applications to visualise single-cell data |
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1-3. Single Cell Analysis Tutorial (Scanpy & Seurat) | Tutorials to describe working with Single Cell data for Scanpy and Seurat: 1. Preprocessing and clustering 3k PBMCs 2. Core Plotting Functions 3. How to preprocess UMI count data with analytic Pearson residuals
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4. Single Cell Tutorial Seurat to AnnData (Scanpy) tutorial | Tutorial demonstrating an example of how a Seurat object can easily be converted to AnnData (Scanpy). |
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5-6. Single Cell Analysis Tutorial (Scanpy) | Tutorials demonstrating how to regress cell cycle effect and how to simulate data using a literature-curated boolean gene regulatory network |
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7-10. Single Cell Analysis Tutorial (Scanpy) Advanced | Tutorials for advanced Single Cell processing. |
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Utilities
Logo | Title | Description | Data Inputs |
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Download data from BaseSpace | Download demultiplexed (fastq.gz) or raw (bcl) Illumina sequencing data through the Illumina BaseSpace CLI. This capsule requires a BaseSpace account and NGS data owned or shared with the user. |
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Sambamba Filtering (Duplicates, Multimappers, Unaligned) | Remove optical and PCR duplicates from Illumina data using the software tool Sambamba. Sambamba is intended to be a drop in replacement for Picard MarkDuplicates but more performant |
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Trim Galore | Trim Galore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data |
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fastp | A tool designed to provide fast all-in-one preprocessing for FastQ files (adapter trimming, downsampling etc.). This tool is developed in C++ with multithreading supported to afford high performance |
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Other
Title | Description | Input Data | |
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MACS PeakCalling | MACS3 is a peak calling tool generally used on ChIP seq data to identify transcript factor binding sites. |
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featureCounts | This capsule will run featureCounts from the Subreads R package to generate an expression matrix. |
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HOMER | Homer contains a useful, all-in-one program for performing peak annotation called annotatePeaks.pl. This capsule uses annotatePeaks.pl to annotate *.bed coordinates with gene features. |
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Gene Enrichment Analysis (GEA) | This capsule presents a user-friendly Streamlit application designed to facilitate gene enrichment analysis. The analysis results are sourced from reliable and widely-used platforms, namely g-profiler and Panther. |
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GATK RNAseq short variant discovery (SNPs + Indels) | Based on GATK RNASeq short variant discovery pipeline. Takes in alignments and outputs vcf containing SNPs and indels |
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Delly somatic complete analysis | This capsule does structural variant (SV) prediction to can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. |
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Delly germline complete analysis | This capsule does structural variant (SV) prediction to discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data |
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ART-Simulation-Illumina | ART is a set of simulation tools to generate synthetic next-generation sequencing reads. |
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PySpark and EMR Serverless | This capsule runs an example PySpark job on EMR Serverless. |
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