News and Announcements » – Make FASTQ file for ERA submission from paired FASTA and QUAL files


The ERA currently requires a separate FASTQ file for each library, split by library id. This code takes the output from and the corresponding QUAL files and produces ERA-compatible FASTQ files.

Usage: [options]

Input Arguments:



-f, --input_fasta_fp
Path to the input fasta file
-q, --qual
Names of QUAL files, comma-delimited


-o, --result_fp
Path to store results [default: <input_sequences_filename>.fastq]
-s, --split
Make separate file for each library [default:False]


Matches QUAL info to FASTA entries by id, and writes FASTQ output to one file or to per-library files.

The FASTQ format for each record is as follows:

@seq_id [and optional description] seq as bases + [and optionally with repeat of seq_id and repeat line] qual scores as string of chr(33+qual)


Take input FASTA file input_fasta_filepath and QUAL file input_qual_filepath: make separate file for each library (with the -s option: assumes that the FASTA file is the output of or similar script): -f $PWD/seqs.fna -q $PWD/Fasting_Example.qual -s