Fastx_renamer allows to rename sequences and either to use the nucleotides sequence as the name or simply use counter as the name. This tool can work both with fasta or fastq files
Parent program: fastx_toolkit
FASTX-Toolkit is a software package for preprocessing output data produced by Next-Generation sequencing machines in FASTA and FASTQ format before the main processing (assembling, mapping etc.). FASTQ to FASTA conversion, statistics calculation, file customization, quality-based preprocessing, trimming and etc. can be provided.