File Formats
The format name usually denotes the file suffix.
FASTA files (suffix: .fasta, .fna, .fa) store sequencing data.
FASTQ files (suffix: .fastq) include sequencing data and quality scores.
SAM/BAM files (suffix: .sam/.bam) were developed for next-generation sequencing (NGS) data. SAM stands for Sequence Alignment Map. These files are used to store alignment information.
VCF (suffix: .vcf) stands for Variant Call Format. These files are used to store information about genetic variants.
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GFF3 (suffix: .gff3) stands for Generic Feature Format (version 3). These files are used to store information about genomic features.
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BED (suffix: .bed) stands for Browser Extensible Data format. These files are used to store genomic regions.
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FASTA Format
A FASTA file begins with a header line, indicated by the > symbol, that contains an identifier and optional description The following lines contain the biological sequence itself.
> NP_000552.2 Human glutathione transferase M1 (GSTM1) MPMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNLPYLIDGAHKITQSNAILCYIARKHNLCGETEEEKIRVDILENQTMDNHMQLGMICYNPEFEKLKPKYLEELPEKLKLYSEFLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPNLKDFISRFEGLEKISAYMKSSRFLPRPVFSKMAVWGNK
FASTQ Format
FASTQ files are helpful for base calling, quality control, and trimming.
Most sequencing tools return data in FASTQ format with quality scores included (ASCII code).
FASTQ files contain four lines:
- ID, beginning with
@ - Sequence
- Description line (typically a
+) - Base qualities in ASCII format
@SEQ_ID
GATTTGGGGTTCAAAGCAGTATCGATCAAATA
+
!''*((((***+))%%%++)(%%%%).1***-
FASTQ File Example: Multiple Reads
@M00747:32:000000000-A16RG:1:1112:15153:29246 1:N:0:1
TCGATCGAGTAACTCGCTGCTGTCAGACTGGTTTTTGGTCGATCGACTATTGTTTCAGTCGCAAGAATATTGTGTCCAGTCGATCGACTGAATTCTGCTGTACGGCCACGGCGGATGCACGGTACAGCAGGCTCAGACGGATTAAACTGTT
+
5=9=9<=9,-5@<<55>,6+8AC>EE.88AE9CDD7>+7.CC9CD+++5@=-FCCA@EF@+**+*--55--AA---AA-5A<9C+3+<9)4++=E=+===<D94)00=9)))2@624(/(/2/-(.(6;9(((((.(.'((6-66<6(///
@M00747:32:000000000-A16RG:1:1112:15536:29246 1:N:0:1
GTAAAATTGAGGTAAATTGTGCGGAATTTAGCAATACCGTTTTTTTTATTATCACCGGATATCTATTCTGCTGTACGGCCAAGGAGGATGTACGGTACAGCAGGTGCGAACTCACTCCGACGCTCAAGTCAGTGACTTAATGATAAGCGTG
+
?????<BBBBBB5<?BFFFFFFECHEFFECCFF?9AAC>7@FHHHHHHFG?EAFGF@EEDEHHDGHHCBDFFGDFHF)<CCD@F,+3=CFBDFHBD++??DBDEEEDE:):CBEEEBCE68>?))5?**0?:AE*A*0//:/*:*:**.0)
@M00747:32:000000000-A16RG:1:1112:15513:29246 1:N:0:1
GCTAGTCTTGTGTTTAGTTTTATGTTTTGCATGTTGTAACGGATTCATAAACATAGGTGTTTGTTTCTTTTTATGGTTGTACAATTTGGCCCTAAGGCCCTACACTTACTTGTTTGTTTCTTTTATGGTACGACATTTGAGTGGTGGTTGA
+