Datasets
=========

We provide multiple data sets for testing purposes. For topology, genome phasing, and genome assembly, we provide the GM12878 cell line. To download one of the data sets, simply use the wget command:

.. code-block:: console

   wget https://s3.amazonaws.com/dovetail.pub/LinkPrep/fastqs/LinkPrep_10M_R1.fastq.gz
   wget https://s3.amazonaws.com/dovetail.pub/LinkPrep/fastqs/LinkPrep_10M_R2.fastq.gz
 
For testing purposes, we recommend using the 10M reads data sets, for any other purpose we recommend using the 800M reads data set.

+-----------------------+-----------------------------------------------------------------------------------+
| Library               | Link                                                                              |
+=======================+===================================================================================+
| GM12878 LinkPrep 10M  | - https://s3.amazonaws.com/dovetail.pub/LinkPrep/fastqs/LinkPrep_10M_R1.fastq.gz  |
|                       | - https://s3.amazonaws.com/dovetail.pub/LinkPrep/fastqs/LinkPrep_10M_R2.fastq.gz  |
+-----------------------+-----------------------------------------------------------------------------------+
| GM12878 LinkPrep 400M | - https://s3.amazonaws.com/dovetail.pub/LinkPrep/fastqs/LinkPrep_R2.fastq.gz      |
|                       | - https://s3.amazonaws.com/dovetail.pub/LinkPrep/fastqs/LinkPrep_R1.fastq.gz      |
|                       | - https://s3.amazonaws.com/dovetail.pub/LinkPrep/fastqs/LinkPrep_R2.fastq.gz      |
+-----------------------+-----------------------------------------------------------------------------------+

For variant detection we also provide two cancer cell lines. To download one of the data sets, simply use the wget command:

.. code-block:: console

   wget https://s3.amazonaws.com/dovetail.pub/VariLink/fastqs/K562.1x.R1.fastq.gz
   wget https://s3.amazonaws.com/dovetail.pub/VariLink/fastqs/K562.1x.R2.fastq.gz
 
For testing purposes, we provide a shallow depth (1X) dataset using the K562 cell line.

+-----------------------+-----------------------------------------------------------------------------------+
| Library               | Link                                                                              |
+=======================+===================================================================================+
| K562 1x               | - https://s3.amazonaws.com/dovetail.pub/VariLink/fastqs/K562.1x.R1.fastq.gz       |
|                       | - https://s3.amazonaws.com/dovetail.pub/VariLink/fastqs/K562.1x.R2.fastq.gz       |
+-----------------------+-----------------------------------------------------------------------------------+

In addition, we provide a higher depth (approx. 30X) dataset using the HCC1187 breast cancer cell line. The list
below provides links to the raw FastQs, BAM file (aligned to hg38), cooler / hic files, and the results generated by 
CNVKit, HiC-Breakfinder, and DeepVariant on this dataset.

+-----------------------+------------------------------------------------------------------------------------------------------+
| Library               | Link                                                                                                 |
+=======================+======================================================================================================+
| HCC1187 30x           | - https://s3.amazonaws.com/dovetail.pub/VariLink/HCC1187/fastqs/HCC1187.R1.fastq.gz                  |
|                       | - https://s3.amazonaws.com/dovetail.pub/VariLink/HCC1187/fastqs/HCC1187.R2.fastq.gz                  |
|                       | - https://s3.amazonaws.com/dovetail.pub/VariLink/HCC1187/analysis/bam/HCC1187.bam                    |
|                       | - https://s3.amazonaws.com/dovetail.pub/VariLink/HCC1187/analysis/cooler/HCC1187.mcool               |
|                       | - https://s3.amazonaws.com/dovetail.pub/VariLink/HCC1187/analysis/hicFiles/HCC1187.hic               |
|                       | - https://s3.amazonaws.com/dovetail.pub/VariLink/HCC1187/analysis/cnvkit/HCC1187.cnr                 |
|                       | - https://s3.amazonaws.com/dovetail.pub/VariLink/HCC1187/analysis/cnvkit/HCC1187.cns                 |
|                       | - https://s3.amazonaws.com/dovetail.pub/VariLink/HCC1187/analysis/hic_breakfinder/HCC1187.breaks.txt |
|                       | - https://s3.amazonaws.com/dovetail.pub/VariLink/HCC1187/analysis/deepvariant/HCC1187.vcf.gz         |
+-----------------------+------------------------------------------------------------------------------------------------------+