Enum: SequenceFileFormat

Standard file formats used for storing sequence data

URI: valuesets:SequenceFileFormat

Permissible Values

Value	Meaning	Description
FASTA	EDAM:format_1929	FASTA sequence format
FASTQ	EDAM:format_1930	FASTQ sequence with quality format
SAM	EDAM:format_2573	Sequence Alignment Map format
BAM	EDAM:format_2572	Binary Alignment Map format
CRAM	None	Compressed Reference-oriented Alignment Map
VCF	EDAM:format_3016	Variant Call Format
BCF	EDAM:format_3020	Binary Variant Call Format
GFF3	None	Generic Feature Format version 3
GTF	None	Gene Transfer Format
BED	None	Browser Extensible Data format
BIGWIG	None	BigWig format for continuous data
BIGBED	None	BigBed format for interval data
HDF5	None	Hierarchical Data Format 5
SFF	EDAM:format_3284	Standard Flowgram Format (454)
FAST5	None	Fast5 format (Oxford Nanopore)
POD5	None	POD5 format (Oxford Nanopore, newer)

Slots

Name	Description
sequence_file_format	Standard file formats used for storing sequence data

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/linkml/valuesets

LinkML Source

name: SequenceFileFormat
description: Standard file formats used for storing sequence data
title: Sequence File Formats
from_schema: https://w3id.org/linkml/valuesets
rank: 1000
permissible_values:
  FASTA:
    text: FASTA
    description: FASTA sequence format
    meaning: EDAM:format_1929
    annotations:
      extensions:
        tag: extensions
        value: .fa, .fasta, .fna, .ffn, .faa, .frn
      content:
        tag: content
        value: sequences only
  FASTQ:
    text: FASTQ
    description: FASTQ sequence with quality format
    meaning: EDAM:format_1930
    annotations:
      extensions:
        tag: extensions
        value: .fq, .fastq
      content:
        tag: content
        value: sequences and quality scores
  SAM:
    text: SAM
    description: Sequence Alignment Map format
    meaning: EDAM:format_2573
    annotations:
      extensions:
        tag: extensions
        value: .sam
      content:
        tag: content
        value: aligned sequences (text)
  BAM:
    text: BAM
    description: Binary Alignment Map format
    meaning: EDAM:format_2572
    annotations:
      extensions:
        tag: extensions
        value: .bam
      content:
        tag: content
        value: aligned sequences (binary)
  CRAM:
    text: CRAM
    description: Compressed Reference-oriented Alignment Map
    annotations:
      extensions:
        tag: extensions
        value: .cram
      content:
        tag: content
        value: compressed aligned sequences
  VCF:
    text: VCF
    description: Variant Call Format
    meaning: EDAM:format_3016
    annotations:
      extensions:
        tag: extensions
        value: .vcf
      content:
        tag: content
        value: genetic variants
  BCF:
    text: BCF
    description: Binary Variant Call Format
    meaning: EDAM:format_3020
    annotations:
      extensions:
        tag: extensions
        value: .bcf
      content:
        tag: content
        value: genetic variants (binary)
  GFF3:
    text: GFF3
    description: Generic Feature Format version 3
    annotations:
      extensions:
        tag: extensions
        value: .gff, .gff3
      content:
        tag: content
        value: genomic annotations
  GTF:
    text: GTF
    description: Gene Transfer Format
    annotations:
      extensions:
        tag: extensions
        value: .gtf
      content:
        tag: content
        value: gene annotations
  BED:
    text: BED
    description: Browser Extensible Data format
    annotations:
      extensions:
        tag: extensions
        value: .bed
      content:
        tag: content
        value: genomic intervals
  BIGWIG:
    text: BIGWIG
    description: BigWig format for continuous data
    annotations:
      extensions:
        tag: extensions
        value: .bw, .bigwig
      content:
        tag: content
        value: continuous genomic data
  BIGBED:
    text: BIGBED
    description: BigBed format for interval data
    annotations:
      extensions:
        tag: extensions
        value: .bb, .bigbed
      content:
        tag: content
        value: genomic intervals (indexed)
  HDF5:
    text: HDF5
    description: Hierarchical Data Format 5
    annotations:
      extensions:
        tag: extensions
        value: .h5, .hdf5
      content:
        tag: content
        value: multi-dimensional arrays
  SFF:
    text: SFF
    description: Standard Flowgram Format (454)
    meaning: EDAM:format_3284
    annotations:
      extensions:
        tag: extensions
        value: .sff
      content:
        tag: content
        value: 454 sequencing data
      status:
        tag: status
        value: legacy
  FAST5:
    text: FAST5
    description: Fast5 format (Oxford Nanopore)
    annotations:
      extensions:
        tag: extensions
        value: .fast5
      content:
        tag: content
        value: nanopore raw signal data
  POD5:
    text: POD5
    description: POD5 format (Oxford Nanopore, newer)
    annotations:
      extensions:
        tag: extensions
        value: .pod5
      content:
        tag: content
        value: nanopore raw signal data (compressed)