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fqlink

fqlink is a small command-line utility to help you retrieve ENA fastq links from NCBI accession codes. The input is provided through STDIN with each line representing an NCBI accession code (srx, srr, gsm) and an optional related name, separated by whitespace (space, tab, etc.). The output is either in the aria2 input file format or Aspera download info JSON format.

Table of Contents

• Installation
• Usage
• Options
• Troubleshooting
• Notes
• License

Installation

Download the binary from release, put it wherever in your PATH.

You can also use cargo to install from GitHub:

cargo install --git https://github.com/TTTPOB/fqlink.git

Usage

Read from STDIN, and print to STDOUT

fqlink [OPTIONS] <input_file >output_file

The output file can then be used in aria2c

aria2c -x16 -s16 -k1m -i output_file

Input:

• Accession codes (srx, srr, gsm) and related (optional) names, names should not contain whitespace
• Tags should be whitespace (space, tab, etc.) delimited
• One item per line

Example input:

SRR123456 SampleNameA
SRR654321 SampleNameB

Options

Option	Description
-a, --ascp	Print Aspera download info JSON; the default output format is aria2 input file format

Notes

The Aspera download info JSON output is intended for use with another under-developing tool. It is not available yet.

License

MIT