Open tseemann opened 5 years ago
Hi Torsten. You are correct that fastq is for short reads and fasta for contigs. Indeed it will not currently handle short reads in fasta format, but that's partly by design, as without the quality information the filtering is not possible. I'll think about the best way to improve this, either by renaming the methods, or allowing fasta/fastq to have an option for the user to specify if the data are short reads or assemblies.
Due to differences inc ommand line parameters, I assume
fastq
is actually for short sequence reads, andfasta
for contigs?What if my reads are in FASTA format? Will
fastq
barf ?