from Bio import SeqIO records = SeqIO.parse("THIS_IS_YOUR_INPUT_FILE.fastq", "fastq") count = SeqIO.write(records, "THIS_IS_YOUR_OUTPUT_FILE.fasta", "fasta") print("Converted %i records" % count) Or you can use this site as online fastq to fasta converter by selecting your format...
(http://maq.sourceforge.net/) And many many others. However, It is sometimes more productive to preprocess the FASTA/FASTQ files before mapping the sequences to the genome - manipulating the sequences to produce better mapping results. The FASTX-Toolkit tools perform some of these preprocessing...
NCBI Blaster(aka BLAST Robot) is a software tool that automates the NCBI BLAST search processes. SFF/FastQ Sequence Workbenchis an efficient and easy to use FastQ/SFF file viewer, editor, filter and converter. Plans for next version Job summary (graphic reports) Multi-threading Feedback/News ...