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

Don’t install it with BioConda!!!
Don’t install it with BioConda!!!
Don’t install it with BioConda!!!

I tried it at 2023/11/29 and 2024/06. 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

sra to fastq

fastq-dump is a command-line utility within the SRA Toolkit that converts SRA (Sequence Read Archive) files into FASTQ format. FASTQ is a widely used file format for storing nucleotide sequences along with their quality scores. This tool allows researchers to extract and utilize raw sequencing data from SRA databases for further analysis.

fastq-dump --split-files --gzip SRRXXXXXXX

The --split-files argument in fastq-dump is specifically related to paired-end sequencing data. It splits the output into two FASTQ files, one for each read of the pair (e.g., your_file_1.fastq and your_file_2.fastq). It was suggested to add the --split-3 parameter at the same time so the unpaired reads could go to the *.fastq file, while the paired reads would go to the *_1.fastq and *_2.fastq.

If you are handling single-end sequencing data, you can ignore this parameter as it is not needed. The output will be a single FASTQ file containing all the reads.

For third-generation sequencing data (such as those produced by PacBio or Oxford Nanopore technologies), there are a few special considerations and parameters to keep in mind:

1. PacBio Data:

   • Use --skip-technical to skip technical reads.
   • Use --clip to remove adapter sequences.

   fastq-dump --skip-technical --clip your_file.sra

2. Oxford Nanopore Data:

   • Use --readids to include read IDs in the output.
   • Use --minReadLen to set a minimum read length to filter out shorter reads.

   fastq-dump --readids --minReadLen 1000 your_file.sra

These parameters help in properly extracting and preparing the data for downstream analysis, ensuring that the specific characteristics of third-generation sequencing reads are adequately handled.

Faster?? My sra file is very large, the fastq-dump takes lots of time for single file, is there any way to speed it up?

• Unfortunately, fastq-dump could not run in multiple threads. So, it reach its fast already.
• Good news is you could also use fasterq-dump from the same package which comes from the same tool packs. Here is an example:
  • fasterq-dump --split-files --threads 8 your_file.sra

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