Algorithms

amino_acid_changes Amino Acid Changes
annotate_against_database_track Annotate with Database Variants
annotate_conservation_score Annotate with Conservation Score
annotate_exon_numbers Exon number annotation
annotate_overlapping Annotate from Overlapping Annotations
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
convert_from_tracks Convert From Tracks
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_variant_database Filter against Database Variants
filter_annotation_names Filter Annotations on Name
filter_haplotype_comparison Variant haplotype compare filter
filter_marginal_variants Filter Marginal Variant Calls
filter_overlapping Filter against Overlapping Annotations
find_primer_binding_sites Find Binding Sites and Create Fragments
fisher_exact_test Fisher comparison
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_mappings Merge Read Mappings
merge_tracks Merge Annotation Tracks
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
ngs_import_tabular Import Tabular Alignments
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
trim Trim Sequences


Subsections