Welcome to Genomkit’s documentation!

Note

This project is under active development.

Genomkit is designed as a collection of modules and functions to handle various file types in bioinformatic analyses. Each file type in fact represents an aspect of the real biological networks. Just as a diamond has many facets, the real biological system has also many views according to the measurement methods.

Although many sophisticated tools or pipelines have been developed for each file type, there isn’t a well-known tool for integrating all of them and providing a convenient way to explore all the file types. Genomkit offers the basic building blocks for further exploring the data or developing any new tools. Below is the scheme of all the modules in Genomkit:

In addition, we aim to make all the operations in Genomkit efficient in memory usage and fast in speed with optimized codes and parallel computing out of the box.

Contents

• Concept
• Usages
  • Installation
• Tutorials
  • Starting with a FASTA file
    • Extract the sequences in FASTA format from the genome sequence by a BED files
  • Starting a FASTQ file
    • Trimming a FASTQ file for both sequences and quality
  • Starting with a BED file
    • Get the sequences in FASTA format from a BED file
    • Get TSSs (Transcription Start Sites) and TTSs (Transcription Termination Sites) of genes in a BED file
    • Merging the nearby peaks in a BED file
    • Sampling the regions randomly in a BED file
    • Find the peaks in one BED file close to the regions in another BED file
    • Generate a heapmap from two BED files: one BED file is used as windows and the other used as the signal
  • Starting with many BED files
    • Test the relevance of multiple peaks in BED files to different biotypes in GTF
  • Starting with a GTF file
    • Get all the genes from a GTF file
    • Extract exon, intron, and intergenetic regions in BED format from a GTF file
    • Get all promoter regions in BED format from a GTF file
    • Extract the genes by their biotypes from a GTF file
• API of GenomKit
  • Genomic Sequences
    • GSequence
      • GSequence.complement()
      • GSequence.count_table()
      • GSequence.dna2rna()
      • GSequence.reverse()
      • GSequence.reverse_complement()
      • GSequence.rna2dna()
      • GSequence.slice_sequence()
      • GSequence.trim()
    • GSequences
      • GSequences.add()
      • GSequences.complement()
      • GSequences.count_table()
      • GSequences.dna2rna()
      • GSequences.extract_seqs_by_regions()
      • GSequences.get_sequence()
      • GSequences.load()
      • GSequences.reverse()
      • GSequences.reverse_complement()
      • GSequences.rna2dna()
      • GSequences.trim()
  • Genomic Alignments
    • GAlignments
      • GAlignments.calculate_coverage()
      • GAlignments.load_reads()
  • Genomic Regions
    • GRegion
      • GRegion.bed_entry()
      • GRegion.distance()
      • GRegion.extend()
      • GRegion.extend_fold()
      • GRegion.overlap()
      • GRegion.resize()
    • GRegions
      • GRegions.add()
      • GRegions.close_regions()
      • GRegions.cluster()
      • GRegions.extend()
      • GRegions.extend_fold()
      • GRegions.filter_by_names()
      • GRegions.filter_by_score()
      • GRegions.get_GSequences()
      • GRegions.get_names()
      • GRegions.get_sequences()
      • GRegions.intersect()
      • GRegions.load()
      • GRegions.merge()
      • GRegions.remove_by_names()
      • GRegions.remove_duplicates()
      • GRegions.resize()
      • GRegions.sampling()
      • GRegions.sort()
      • GRegions.split()
      • GRegions.subtract()
      • GRegions.total_coverage()
      • GRegions.write()
    • GRegionsSet
      • GRegionsSet.add()
      • GRegionsSet.combine()
      • GRegionsSet.count_overlaps()
      • GRegionsSet.get_lengths()
      • GRegionsSet.get_names()
      • GRegionsSet.load_pattern()
      • GRegionsSet.subtract()
  • Genomic Annotation
    • GAnnotation
      • GAnnotation.filter_elements()
      • GAnnotation.get_exon()
      • GAnnotation.get_exon_ids()
      • GAnnotation.get_gene()
      • GAnnotation.get_gene_ids()
      • GAnnotation.get_gene_names()
      • GAnnotation.get_regions()
      • GAnnotation.get_transcript()
      • GAnnotation.get_transcript_ids()
      • GAnnotation.load_data()
  • Genomic Coverages
    • GCoverages
      • GCoverages.calculate_coverage_GRegions()
      • GCoverages.calculate_coverage_GRegions2()
      • GCoverages.calculate_coverage_from_bam()
      • GCoverages.filter_regions_coverage()
      • GCoverages.flip_negative_regions()
      • GCoverages.get_coverage()
      • GCoverages.get_dataframe()
      • GCoverages.load_coverage_from_bigwig()
      • GCoverages.scale_coverage()
      • GCoverages.total_sequencing_depth()
    • GCoveragesSet
      • GCoveragesSet.add()
      • GCoveragesSet.flip_negative_regions()
      • GCoveragesSet.get_names()
  • Genomic Variants
    • GVariants
      • GVariants.load()
      • GVariants.to_GRegions()