sratools

sratools

GitHub

There are some dependency problems. So, conda would be the easist way to get this tool.

Install

conda install -c bioconda sra-tools

I tried it at 2023/11/29. It could download 2.8 automatically but prefetch doesn’t work. So, please use the way below.

Or download and configure

wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/3.0.0/sratoolkit.3.0.0-ubuntu64.tar.gz
tar -xvzf sratoolkit.3.0.0-ubuntu64.tar.gz

# if you are using bash environment rather than zsh, change zshrc tp bashrc
echo PATH=\$PATH:$(pwd)/sratoolkit.3.0.0-ubuntu64/bin >> ~/.zshrc
source ~/.zshrc

#configure sratools
vdb-config --interactive

After executing vdb-config, you can see an interactive environment board as below. You can input c to select CACHE. You can also select it by mouse and then input enter. Then, you need to give a directory for the category:

process-local location:
-[choose]
+[choose] /tmp

After that, save your change and you can use sratools, now.

SRA data download

prefetch  --ascp-path "/usr/bin/ascp|/home/ken/.aspera/connect/etc/asperaweb_id_dsa.putty" ERR02559

For trinity

fastq-dump --defline-seq '@$sn[_$rn]/$ri' --split-files file.sra

Trinity --seqType fq --max_memory 55G --single Seq.fastq --CPU 8 --full_cleanup