Enum: SequenceFileFormat

Standard file formats used for storing sequence data

URI: valuesets:SequenceFileFormat

Permissible Values

Value	Meaning	Description	Content	Extensions	Status
FASTA	EDAM:format_1929	FASTA sequence format	sequences only	.fa, .fasta, .fna, .ffn, .faa, .frn
FASTQ	EDAM:format_1930	FASTQ sequence with quality format	sequences and quality scores	.fq, .fastq
SAM	EDAM:format_2573	Sequence Alignment Map format	aligned sequences (text)	.sam
BAM	EDAM:format_2572	Binary Alignment Map format	aligned sequences (binary)	.bam
CRAM		Compressed Reference-oriented Alignment Map	compressed aligned sequences	.cram
VCF	EDAM:format_3016	Variant Call Format	genetic variants	.vcf
BCF	EDAM:format_3020	Binary Variant Call Format	genetic variants (binary)	.bcf
GFF3		Generic Feature Format version 3	genomic annotations	.gff, .gff3
GTF		Gene Transfer Format	gene annotations	.gtf
BED		Browser Extensible Data format	genomic intervals	.bed
BIGWIG		BigWig format for continuous data	continuous genomic data	.bw, .bigwig
BIGBED		BigBed format for interval data	genomic intervals (indexed)	.bb, .bigbed
HDF5		Hierarchical Data Format 5	multi-dimensional arrays	.h5, .hdf5
SFF	EDAM:format_3284	Standard Flowgram Format (454)	454 sequencing data	.sff	legacy
FAST5		Fast5 format (Oxford Nanopore)	nanopore raw signal data	.fast5
POD5		POD5 format (Oxford Nanopore, newer)	nanopore raw signal data (compressed)	.pod5

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
instantiates:
- valuesets_meta:ValueSetEnumDefinition
description: Standard file formats used for storing sequence data
title: Sequence File Formats
from_schema: https://w3id.org/linkml/valuesets
contributors:
- orcid:0000-0002-6601-2165
- https://github.com/anthropics/claude-code
status: DRAFT
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)