seqkit stats generates statistics about sequencing read files.
Where:
Run seqkit stats in the same folder as your read files.
Input:
read files (eg. .fastq.gz): Before opening this menu,
select one or more read files.
Files may be gzipped or uncompressed.
Number of threads to use:
Because seqkit
uses pigz to uncompress files, the number of files that can be
uncompressed at one time is dependent on the number of CPUs
utilized.
Performance note: As the # of CPUs increase, the
load on RAM also increases, because SeqKit uses pigz to do
decompression through an I/O stream for each file. It could
be that things will go faster if we use a smaller number of
CPUs. Some experimentation may be needed to optimize speed.
Output:
Output is written to the input directory.
Output will also pop up in a new blreads window with the
statistics from each file in table format. For most programs in
BioLegato that take sequencing reads as input, you can probably
select all files in the output window and then launch the next
program.