Chart of data format conversions with Kent source utilites

Kent source utilities are the part of the UCSC Genome Browser and implement a number of tasks related to bioinformatic data analysis. In particular, they can be used to convert genomic data files from one format to another.

The chart below shows what formats can be converted to each other using Kent source utilities; each edge corresponds to a single tool.

 

kent_utilities_graph

The following formats are considered on the chart:

  • 2bit – a binary randomly-accessible format for storing DNA sequences;
  • Axt – a sequence alignment format used by Blastz;
  • BED – a general-purpose tabular format for storing genomic features;
  • bedGraph – an extension version of the BED format to store continuous-valued data;
  • bigBed – an indexed binary format based on the BED format;
  • bigGenePred – an indexed binary format based on the GenePred format;
  • bigWig – an indexed binary format based on the WIG format;
  • Chain – a pairwise alignment format allowing gaps in both sequences;
  • FASTA – a plain-text format for storing multiple sequences;
  • FASTQ – a plain-text format for storing multiple sequences with base quality values;
  • GenePred – a gene prediction track format;
  • GFF3 – a general-purpose format for genomic features of different kind with various attributes;
  • GTF – a gene annotation format describing exons, transcripts and genes;
  • LAV – a plain-text format for alignments of a pair of DNA sequences used by Blastz;
  • MAF – a multiple alignment format;
  • Net – a format for the net alignment annotations used in the UCSC Genome Browser;
  • PSL – an alignment format that BLAT results are usually converted to;
  • WIG – a track format for storing continuous-values data.

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