- About the Workflow Designer
- Introduction
- Manipulating Element
- Manipulating Workflow
- Changing Appearance
- Custom Elements with Scripts
- Custom Elements with Command Line Tools
- Using Script to Set Parameter Value
- Running Workflow from the Command Line
- Running Workflow in Debugging Mode
- Workflow File Format
- Workflow Elements
- Data Readers
- Data Writers
- Data Flow
- Basic Analysis
- Amino Translations Element
- Annotate with DAS Element
- Annotate with UQL Element
- CD-Search Element
- Collocation Search Element
- Export PHRED Qualities Element
- Fetch Sequences by ID From Annotation Element
- Filter Annotation by Name Element
- Filter Annotations by Qualifier
- Find Correct Primer Pairs Element
- Find Pattern Element
- Find Repeats Element
- Gene-by-gene approach report
- Get Sequences by Annotations Element
- Group Primer Pairs Element
- Import PHRED Qualities Element
- Local BLAST Search Element
- Local BLAST+ Search Element
- Merge Annotations Element
- ORF Marker Element
- Remote BLAST Element
- Smith-Waterman Search Element
- Data Converters
- DNA Assembly
- HMMER2 Tools
- HMMER3 Tools
- Includes
- Multiple Sequence Alignment
- Align Profile to Profile with MUSCLE Element
- Align to Reference Element
- Align with ClustalO Element
- Align with ClustalW Element
- Align with Kalign Element
- Align with MAFFT Element
- Align with MUSCLE Element
- Align with T-Coffee Element
- Extract Consensus from Alignment as Sequence
- Extract Consensus from Alignment as Text
- Join Sequences into Alignment Element
- Split Alignment into Sequences Element
- NGS: Align Short Reads
- NGS Basic
- Assemble Genomes with SPAdes Element
- CASAVA FASTQ Filter Element
- Cut Adapter Element
- Extract Consensus from Assembly Element
- Extract Coverage from Assembly Element
- FASTQ Merger Element
- FASTQ Quality Trimmer Element
- FastQC Quality Control Element
- Filter BAM/SAM Files Element
- Genome Coverage Element
- Merge BAM Files Element
- Remove Duplicates in BAM Files Element
- Slopbed Element
- Sort BAM Files Element
- NGS: ChiP-Seq Analysis
- NGS: RNA-Seq Analysis
- NGS: Variant Calling
- SNP Annotation
- Transcription Factor
- Build Frequency Matrix Element
- Build SITECON Model Element
- Build Weight Matrix Element
- Convert Frequency Matrix Element
- Read Frequency Matrix Element
- Read SITECON Model Element
- Read Weight Matrix Element
- Search for TFBS with SITECON Element
- Search for TFBS with Weight Matrix Element
- Write Frequency Matrix Element
- Write SITECON Model Element
- Write Weight Matrix Element
- Utils
- Custom Elements With Script
- Workflow Samples
- Alignment
- Conversions
- Custom elements
- Data Marking
- Data Merging
- HMMER
- NGS
- Assembly with Spades
- Call Variants with SAMtools
- ChIP-Seq Coverage
- ChIP-seq Analysis with Cistrome Tools
- Extract Consensus from Assembly
- Extract Coverage from Assembly
- Extract Transcript Sequences
- Quality Control by FastQC
- Raw ChIP-Seq Processing
- Raw DNA-Seq Processing
- Raw RNA-Seq Processing
- RNA-seq Analysis with Tuxedo Tools
- Variation Annotation with SnpEff
- Sanger Sequencing
- Scenarios
- Transcriptomics
- Data Readers
- Data Writers
- Data Flow
- Basic Analysis
- Amino Translations Element
- Annotate with DAS Element
- Annotate with UQL Element
- CD-Search Element
- Collocation Search Element
- Export PHRED Qualities Element
- Fetch Sequences by ID From Annotation Element
- Filter Annotation by Name Element
- Filter Annotations by Qualifier
- Find Correct Primer Pairs Element
- Find Pattern Element
- Find Repeats Element
- Gene-by-gene approach report
- Get Sequences by Annotations Element
- Group Primer Pairs Element
- Import PHRED Qualities Element
- Local BLAST Search Element
- Local BLAST+ Search Element
- Merge Annotations Element
- ORF Marker Element
- Remote BLAST Element
- Smith-Waterman Search Element
- Data Converters
- DNA Assembly
- HMMER2 Tools
- HMMER3 Tools
- Includes
- Multiple Sequence Alignment
- Align Profile to Profile with MUSCLE Element
- Align to Reference Element
- Align with ClustalO Element
- Align with ClustalW Element
- Align with Kalign Element
- Align with MAFFT Element
- Align with MUSCLE Element
- Align with T-Coffee Element
- Extract Consensus from Alignment as Sequence
- Extract Consensus from Alignment as Text
- Join Sequences into Alignment Element
- Split Alignment into Sequences Element
- NGS: Align Short Reads
- NGS Basic
- Assemble Genomes with SPAdes Element
- CASAVA FASTQ Filter Element
- Cut Adapter Element
- Extract Consensus from Assembly Element
- Extract Coverage from Assembly Element
- FASTQ Merger Element
- FASTQ Quality Trimmer Element
- FastQC Quality Control Element
- Filter BAM/SAM Files Element
- Genome Coverage Element
- Merge BAM Files Element
- Remove Duplicates in BAM Files Element
- Slopbed Element
- Sort BAM Files Element
- NGS: ChiP-Seq Analysis
- NGS: RNA-Seq Analysis
- NGS: Variant Calling
- SNP Annotation
- Transcription Factor
- Build Frequency Matrix Element
- Build SITECON Model Element
- Build Weight Matrix Element
- Convert Frequency Matrix Element
- Read Frequency Matrix Element
- Read SITECON Model Element
- Read Weight Matrix Element
- Search for TFBS with SITECON Element
- Search for TFBS with Weight Matrix Element
- Write Frequency Matrix Element
- Write SITECON Model Element
- Write Weight Matrix Element
- Utils
- Custom Elements With Script
- Alignment
- Conversions
- Custom elements
- Data Marking
- Data Merging
- HMMER
- NGS
- Assembly with Spades
- Call Variants with SAMtools
- ChIP-Seq Coverage
- ChIP-seq Analysis with Cistrome Tools
- Extract Consensus from Assembly
- Extract Coverage from Assembly
- Extract Transcript Sequences
- Quality Control by FastQC
- Raw ChIP-Seq Processing
- Raw DNA-Seq Processing
- Raw RNA-Seq Processing
- RNA-seq Analysis with Tuxedo Tools
- Variation Annotation with SnpEff
- Sanger Sequencing
- Scenarios
- Transcriptomics