fastq -> READS ; fasta -> CONTIGS ?

simonrharris / SKA

Split Kmer Analysis

MIT License

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fastq -> READS ; fasta -> CONTIGS ? #15

Open tseemann opened 5 years ago

tseemann commented 5 years ago

Due to differences inc ommand line parameters, I assume fastq is actually for short sequence reads, and fasta for contigs?

What if my reads are in FASTA format? Will fastq barf ?

simonrharris commented 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.