File formats

Commands to convert file formats
FASTA files
FASTQ files
FASTQ file format options
Phred (Quality) scores in FASTQ files
Calculating average Phred (Q) scores is a bad idea
Sequence labels
Annotations in sequence labels
Sequence database files
IUPAC codes for sequence wildcard letters N, X etc.
Why doesn't USEARCH support gzipped FASTQ files?
SAM files
CIGAR strings in SAM files
USEARCH Database (UDB) files
Mothur file formats
QIIME file formats
OTU table file formats
NAST multiple alignment files (nastout)
Newick tree format
Metadata file