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 with Overlap Information
annotate_variant_flank Annotate with Flanking Sequences
annotate_with_gff GFF/GTF/GVF Annotation
assemble_sanger_sequences Assemble Sequences
blast BLAST
blast_make_db Create BLAST Database
blast_ncbi BLAST at NCBI
chip_seq ChIP-Seq Analysis
compare_sample_variant_tracks Compare Sample Variant Tracks
compare_variants_within_group Compare Variants within Group
consensus_sequence_extraction Extract Consensus Sequence
contig_read_mapping Map Reads to Contigs
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
coverage_analysis Coverage Analysis
create_histogram Create Histogram
denovo_assembly De Novo Assembly
detailed_mapping_report Create Mapping Report
detect_components_with_test Detect Components With Test
detect_components_without_test Detect Components Without Test
detect_duplicate_classkeys Detect Duplicate Classkeys Algo
download_genome Download Genome
extract_annotations Extract Annotations
extract_overlapping_reads Extract overlapping reads
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 Based on Overlap
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
graph_threshold Extract Annotations
import_tracks Import Tracks from File
integration_test Integration Server Tester
local_realignment Local Realignment
mapping_graph_tracks Create Mapping Graph Tracks
merge_annotation_tracks Merge Annotation Tracks
merge_mappings Merge Read Mappings
merge_overlapping_pairs Merge Overlapping Pairs
ml_phylogeny Maximum Likelihood Phylogeny
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
reference_assemble_sanger_sequences Assemble Sequences to Reference
reverse_complement_sequence Reverse Complement Sequence
reverse_sequence Reverse Sequence
rna_seq RNA-Seq Analysis
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
structural_variant_detection InDels and Structural Variants
translate_to_protein Translate to Protein
tree_construction Tree Construction
trim Trim Sequences
trio_analysis TRIO analysis

Subsections