From 439eeab45238843949ad2c31186f34adac314fea Mon Sep 17 00:00:00 2001 From: MitraDarja Date: Wed, 9 Aug 2023 13:40:07 +0200 Subject: [PATCH] Add parallelization benchmark --- utils/README.md | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/utils/README.md b/utils/README.md index a151412..c1e4574 100644 --- a/utils/README.md +++ b/utils/README.md @@ -1,4 +1,4 @@ -`# Evaluation of Needle count +# Evaluation of Needle count ## Differential Expression Download the sequencing experiments listed in accession.lst and the human transcripts from gencode as a fasta file. @@ -35,6 +35,15 @@ differential expressed genes from https://doi.org/10.1016/j.dib.2018.03.079. # Evaluation of Needle +## Parallelization + +In order to compare the two parallelization methods of Needle when computing minimizers, four sequencing experiments were tested. +For the simple version the following command was used with either `X=1` or `X=4` threads. +``` +needle minimiser -k 21 -w 25 -t X SRR1313229.fastq.gz SRR1313228.fastq.gz SRR1313227.fastq.gz SRR1313226.fastq.gz +``` +For the ram friendly version a `--ram` was added to the previous command. + ## Differential Expression Download the sequencing experiments of the GEO experiment with the accession number GSE58135 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58135). Then create a Needle index in the following way, assuming all sequencing files are stored in a folder named GSE58135: