Workflow Catalog

Browse our rigorously developed and supported workflows for your field of research.

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Sequence Alignment

Sequence Similarity Search

This workflow can be used to perform sequence similarity search e.g. blast, fasta, ssearch, etc

External Data

Download Data: SRA FastQ Files

This workflow can be used to download publicly available SRA FastQ files

Sequence Alignment
Protein Engineering

Protein Multiple Sequence Alignment

This workflow can be used to perform MSA of homologous protein sequences.

Gene Therapy
Functional Genomics

Predict Structure of a Nucleotide Sequence

This workflow can be used to predict the structure of a nucleotide sequence as well as look for specific structures within the sequence

Candidate Validation
Gene Therapy

AAV PacBio QC

The workflow can be used to assess the quality of AAV production using PacBio Sequencing data, by examining alignment coverage across sequences and sequence regions including promotor and CDS region.

Protein Engineering

Protein Design

This workflow can be used to predict new protein sequence likely to have a protein structure, given the structure of a known protein.

Protein Engineering

Protein Structure and Function: FastA Sequence

This workflow can be used to find publicly available experimentally-derived and predicted structures, determine protein domains, predict protein function and predict 2D- and 3D-structures using a FastA Sequence

De-Extinction
Genome Editing

CRISPR Knock-Out

This workflow designs guide RNA sequences for knock-out experiments.

De-Extinction
Genome Editing

AmpliconSeq: Batch

This workflow performs CRISPResso batch analysis on amplicon sequencing fastqs

Functional Genomics
Next Generation Sequencing

Bismark Methylation Analysis

Determine methylation patterns in Bisulfite-Seq applications

External Data

Build Alignment Indexes for a Genome Assembly

This workflow can be used to create alignment indexes and other resources for running NGS workflows. The workflow create alignment index files for Blast, Minimap2, BWA, Bowtie, Bismark, HiSat2, Star and Salmon. It also makes the BS Genome resource for some bioconductor applications and MSI index to determine microsattelite stability.

Functional Genomics
Next Generation Sequencing

Single Cell Analysis

This workflow is designed to analyze single cell RNASeq data post-mapping and gene annotation

Precision Medicine
Next Generation Sequencing

Genomics: Germline Variant Analysis

This workflow can be used to identify single-nucleotide variants, indels and structural variants in a genomics resequencing project compared to a reference genome

Precision Medicine
Functional Genomics
Next Generation Sequencing

RNASeq: Expression and Fusion Analysis in Human Tumors

This workflow can be used to determine gene abundances, splice variants, gene fusion events, skipped exons and differential expression analysis in human tumors

Precision Medicine
Next Generation Sequencing

Genomics: Somatic Variant Analysis in Human Tumors

This workflow can be used to identify single-nucleotide variants, indels and structural variants in Human Tumor sequencing project compared to a reference genome with or without a normal matched control sample

Precision Medicine
Next Generation Sequencing

Genomics: SARS-Cov-2 Germline Variant Analysis

This workflow can be used to identify single-nucleotide variants, indels and structural variants in COVID-19 genomics sequencing project. This workflow also can determine lineage using Pangolin

Association Studies

GWAS with PLINK

This workflow can be used to perform Genome-Wide Association Studies

Precision Medicine
Next Generation Sequencing

Human Haplotype

Determine the Haplotype of certain genes including HLA, RBG, and Codis

Genomics

Prokaryote Genome Annotation

This workflow can be used to find genes a prokaryote genome

De-Extinction
Next Generation Sequencing

Genomics: Ancient DNA Germline Variant Analysis

This workflow can be used to identify single-nucleotide variants, indels and structural variants in a Ancient DNA genomics resequencing project compared to a reference genome

Genomics

Eukaryote Genome Annotation

This workflow can be used to identify genes and determine gene structure and alternatively spliced forms in a eukaryote genome

Functional Genomics
Next Generation Sequencing

RNASeq: Expression Analysis

This workflow can be used to determine gene abundances, splice variants and differential expression analysis

De-Extinction
Genome Editing
Candidate Validation

CRISPRedict: Genome Editing

This workflow designs sgRNA sequences for CRISPR genome editing experiments. It includes homology directed repair, base editing, and prime editing (3 and 3b)

Candidate Validation
Premium

ForML Candidate Optimization

This Form Bio-customized workflow uses a pre-trained ML model to optimize an AAV nucleotide construct for hairpins, codon bias, and CpG islands.

Candidate Validation
Functional Genomics

Optimize a Nucleotide Sequence

This workflow can be used to optimize a nucleotide sequence for codon usage and folding energies

External Data

Download Data: Get Gene Sequences

This workflow is designed to help the users extract the gene sequences from a genome including the genomic, cds, and protein sequences.

Functional Genomics
Next Generation Sequencing

RNASeq: Compare Alignment Tools

This workflow can be used to determine gene abundances from multiple alignment tools for comparison

Functional Genomics
Next Generation Sequencing

RNASeq: Differential Expression Analysis from Gene Abundance Tables

This workflow has been designed to determine differentially expressed genes, using abundance of transcripts and genes from previous workflow analysis which generates gene and transcript counts

Functional Genomics
Next Generation Sequencing

RNASeq: Recount3 Data Download

This workflow can be used to download count and FPKM data from recount3

Next Generation Sequencing

Genomics: Germline Variant Analysis using a Private Genome

This workflow can be used to identify single-nucleotide variants, indels and structural variants in a genomics resequencing project compared to a reference genome from your project

Next Generation Sequencing

Genomics: Germline Variant Analysis, Start with BAMs

This workflow can be used to identify single-nucleotide variants, indels and structural variants in a genomics resequencing project compared to a reference genome. Input file is BAMs

Protein Engineering
Sequence Alignment

Protein Multiple Sequence Alignment from Database

This workflow can be used to perform MSA of homologous protein sequences from a database.

Protein Engineering

Protein Structure and Function: Protein Accession

This workflow can be used to find publicly available experimentally-derived and predicted structures, determine protein domains, predict protein function and predict 2D- and 3D-structures using a Protein Accession (Uniprot, Refseq, Ensembl)

Sequence Alignment

Sequence Similarity Search with CustomDB

This workflow can be used to perform sequence similarity search e.g. blast, fasta, ssearch, etc with a custom database

Form Bio Resources