Algorithms

`alignment`	Create Alignment
`amino_acid_changes`	Amino Acid Changes
`annotate_conservation_score`	Annotate with Conservation Score
`annotate_exon_numbers`	Exon number annotation
`annotate_from_known_variants`	Annotate from Known Variants
`annotate_overlapping`	Annotate from Overlapping Annotations
`annotate_variant_flank`	Annotate with Flanking Sequences
`blast`	BLAST
`blast_make_db`	Create BLAST Database
`blast_ncbi`	BLAST at NCBI
`chip_seq`	ChIP-Seq Analysis
`compare_variants_within_group`	Compare Variants within Group
`consensus_sequence_extraction`	Extract Consensus Sequence
`convert_from_tracks`	Convert From Tracks
`convert_to_dna`	Convert RNA to DNA
`convert_to_rna`	Convert DNA To RNA
`convert_to_tracks`	Convert To Tracks
`denovo_assembly`	De Novo Assembly
`detailed_mapping_report`	Create Mapping Report
`download_genome`	Download Genome
`extract_sequences`	Extract Sequences
`filter_against_control_reads`	Filter against Control Reads
`filter_against_known_variants`	Filter against Known Variants
`filter_annotation_names`	Filter Annotations on Name
`filter_marginal_variants`	Filter Marginal Variant Calls
`filter_overlapping`	Filter against Overlapping Annotations
`filter_reference_variants`	Filter Reference Variants
`find_open_reading_frames`	Find Open Reading Frames
`find_primer_binding_sites`	Find Binding Sites and Create Fragments
`fisher_exact_test`	Fisher Exact Test
`gc_contents_graph_track`	Create GC Contents Graph Track
`go_enrichment_variants`	GO Enrichment Analysis
`import_tracks`	Import Tracks from File
`mapping_graph_tracks`	Create Mapping Graph Tracks
`merge_annotation_tracks`	Merge Annotation Tracks
`merge_mappings`	Merge Read Mappings
`merge_overlapping_pairs`	Merge Overlapping Pairs
`ngs_import_fasta`	Fasta High-Throughput Sequencing Import
`ngs_import_illumina`	Illumina High-Throughput Sequencing Import
`ngs_import_iontorrent`	Ion Torrent High-Throughput Sequencing Import
`ngs_import_roche454`	Roche 454 High-Throughput Sequencing Import
`ngs_import_sam`	Import SAM/BAM Files
`ngs_import_sanger`	Sanger High-Throughput Sequencing Import
`ngs_import_solid`	Solid High-Throughput Sequencing Import
`predict_splice_site`	Predict Splice Site Effect
`probabilistic_variant_detection`	Probabilistic Variant Detection
`process_tagged_sequences`	Process Tagged Sequences
`quality-based_variant_detection`	Quality-based Variant Detection
`read_mapping`	Read Mapping
`rna_seq`	RNA-Seq
`secondary_peak_calling`	Secondary Peak Calling
`sequencing_qc_report`	Create Sequencing QC Report
`small_rna_annotate`	Annotate and Merge Counts
`small_rna_sampling`	Extract and Count
`statistics_target_regions`	Create Statistics for Target Regions
`translate_to_protein`	Translate to Protein
`trim`	Trim Sequences
`trio_analysis`	TRIO analysis

Subsections