Is there any possibility to run gffread in multi-thread mode? The answer seems to be 'no' from the manual (or
gffread -h), as no multi-thread option is mentioned.
I'm mostly using this utility to extract transcript sequences (FASTA) from annotation files (GTF). In single-thread mode, runtime is acceptable in most cases, but would like to speed up a bit in some cases (especially for big genomes).
Note that I already tried, as mentioned in the manual, to index the genome first (which, again, cuts the runtime in most but not all cases):
Note that the retrieval of the transcript sequences this way is going to be much faster if a fasta index file (genome.fa.fai in this example) is found in the same directory with the genomic fasta file.
Such an index file can be created with the samtools utility prior to running gffread, like this:
samtools faidx genome.fa
Then in subsequent runs using the -g option gffread will find this FASTA index and use it to speed up the extraction of transcript sequences.
I'm also open to different alternatives than
gffread to convert GTF -> FASTA.