fastqToFa [options] in.fastq out.fa
This tool is part of UCSC Genome Browser's utilities.
-nameVerify='Supercontig_'
).-verbose=3
to see warnings).The following command will convert sequencing records in a FASTQ file to FASTA format. First, let's take a quick look at the input FASTQ file:
zcat r1.fastq.gz | head
@E00440:705:HGVNKCCX2:8:1101:18396:2909:GAGAGA_GGCAGT 1:N:0:ATGTCA
GTGCCAGGTGCTCTCTCAACCCCAGCGCAGTCTGT
+
JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ
@E00440:705:HGVNKCCX2:8:1101:19045:2909:TTCTTA_GCAAAC 1:N:0:ATGTCA
GCAACCTTCTCAGAAGTCAGCCGGAAAAG
+
JJJJJJJJJFJJJJJFJJJJFJJJJJJJJ
@E00440:705:HGVNKCCX2:8:1101:19593:2909:AGCATG_CGCGCA 1:N:0:ATGTCA
GCTTCTCCACAGACGCGCGTCGGTTAGGAGAGCTCCACTTGAACCTTCCTTT
then we run the command:
fastqToFa r1.fastq.gz r1.fa
Now check the output FASTA file
head r1.fa
>E00440:705:HGVNKCCX2:8:1101:18396:2909:GAGAGA_GGCAGT 1:N:0:ATGTCA
GTGCCAGGTGCTCTCTCAACCCCAGCGCAGTCTGT
>E00440:705:HGVNKCCX2:8:1101:19045:2909:TTCTTA_GCAAAC 1:N:0:ATGTCA
GCAACCTTCTCAGAAGTCAGCCGGAAAAG
>E00440:705:HGVNKCCX2:8:1101:19593:2909:AGCATG_CGCGCA 1:N:0:ATGTCA
GCTTCTCCACAGACGCGCGTCGGTTAGGAGAGCTCCACTTGAACCTTCCTTT
>E00440:705:HGVNKCCX2:8:1101:20446:2909:CTGGCA_CCTGCA 1:N:0:ATGTCA
GCCTCCTGCTCGGCCAGGTCCGGAAAG
>E00440:705:HGVNKCCX2:8:1101:20770:2909:TATAAA_CCACCC 1:N:0:ATGTCA
AGACCCCGGAACCGCCATGAACAGCCCCCACCAAG