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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

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

You can always use fqlink -h.

Read from STDIN, and print to STDOUT.

fqlink [OPTIONS] <input_file >output_file

The output file can then be used in aria2c, like:

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

License

MIT