fa2fq

Converting FASTA to FASTQ where lower and upper case denoted bases have different expected error rates.

Examplary usecase:
The hybrid long read error correction tool LoRDEC outputs corrected long reads in FASTA-format with upper case characters for corrected regions and lower case characters for uncorrected regions. Long read transcriptome assembly tools such as RATTLE or isON accept or expect long reads in FASTQ-format. Using long reads precorrected with LoRDEC and their expected quality added with fa2fq can improve the accuracy of the resulting assembly.

usage: fa2fq [-h] [-o] [-v] FASTA S s

FASTA to FASTQ conversion

positional arguments:
  FASTA
  S               Expected error rate for bases denoted with upper case characters
  s               Expected error rate for bases denoted with lower case characters

options:
  -h, --help      Show this help message and exit
  -o , --offset   Phred-quality offset (Default: 33)