fastqToFa

Reference Code backup Executable files

Convert from fastq to fasta format

Category

Format Conversion

Usage

fastqToFa [options] in.fastq out.fa

Manual

This tool is part of UCSC Genome Browser's utilities.

Required arguments

  • in.fastq string: Input FASTQ file (this file can be gzip-compressed).
  • out.fa string: Output FASTA file.

Options

  • -nameVerify string: For multi-line FASTQ files, string must match somewhere in the sequence names in order to correctly identify the next sequence block (e.g., -nameVerify='Supercontig_').
  • -qual file.qual.fa: Output quality scores to specified file (default: quality scores are ignored).
  • -qualSizes qual.sizes: Write sizes file for the quality scores.
  • -noErrors: Warn only on problems, do not error out (specify -verbose=3 to see warnings).
  • -solexa: Use Solexa/Illumina quality score algorithm (instead of Phread quality).
  • -verbose 2: Set warning level to get some stats output during processing.

Examples

Convert a FASTQ file to a FASTA file

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

File formats this tool works with
FASTQ

Share your experience or ask a question