Software.

Software to analyse and report on sequins within your NGS libraries.

Please access software (Anaquin) using the following link:

https://github.com/sequinstandards/Anaquin

Anaquin is a command-line software toolkit that can analyse sequin reads, measure diagnostic performance and build visual reports. Please note that this is a beta release and anaquin is under active development with regular version updates. Please report issues to sequin@garvan.org.au

License. Anaquin is available for use under the license terms here. Please read this software licence agreement carefully before using the anaquin software. By using the anaquin software you (the licensee) agree that this agreement is enforceable and your use is subject to these terms.

Installation.  Anaquin requires C++ 11 (version 4.8 higher for gcc) and Python (2 or 3). 

Download the latest anaquin version into your working directory and compile with the following commands:

git clone https://github.com/sequinstandards/Anaquin.git
cd Anaquin
make

Further reading.

Version history.
Current:

Version.3.17.7 (March 1st) – Major new release. Updates to split, meta, rna, calibration, germline and somatic. Upodates include more detailed summary test reports, and new usage. Compatible with all current website protocols (version 5 and higher).

Previous:

Version 3.10.0 (Oct 29th) – Anaquin meta includes trimming on artifactual terminal reads that can occur during Illumina TruSeq library preparation.

Version 3.8.1 (July 25th) – Anaquin tools now generate detailed text output files. Added new calibration options to enable absolute and relative calibration of sequin reads within a library. Patched make error (htslib for libcurl). RAnaquin package also updated

Version 3.6.3 (June 27th) – Added test reporting for anaquin meta. Added support for new metagenome mixtures.

Version 3.5.7 (June 9th) – Updated anaquin calibration report to provide report on sequin performance.

Version 3.4.10 (Apr 19th) – Updated RAnaquin R package with minor patches for graph-plotting functions.

Version 3.4.6 (Apr 16th) – Added a new anaquin rna tool for analysis of RNA sequins (still beta). Added –noflip option to anaquin meta (enables skipping of read re-orientation). Removed installation dependencies (no cmake!). Introduced new calibration options for anaquin meta.

Version 3.3.15 (April 16th) – Added –build option to anaquin calibrate, germline and somatic to supports alternative genome builds (e.g. hg19). Fixed docker script for anaquin.

Version 3.3.1 (April 5th) – Added new tool, anaquin meta, for analysing metagenome sequins. Added new option, ladder_calibration and sequin_calibration to allow the dilution of sequins to be calibrated according to user requirements.

Location of resource files.

Anaquin requires the resource bundle (that contains all the reference files) to be located within the same directory as the program to run. By default, the resource bundle will be unpacked in the same directory as anaquin upon compilation.  However, if you move anaquin to another directory, you must also move the accompanying resource bundle. For example:


mkdir /tmp/MyNewAnaquinFolder
# Copy Anaquin
cp anaquin /tmp/MyNewAnaquinFolder 
# Also copy the resource bundle (the whole folder)
cp -rf resources /tmp/MyNewAnaquinFolder  
# Run Anaquin form the new folder
/tmp/MyNewAnaquinFolder/anaquin