ena-STUDY-UNIVERSITY OF LEEDS-22-08-2018-10:21:11:714-104
This study provides simulated genome sequences, ground truth variant profiles, and whole-exome sequencing reads for artificial tumour bulk samples, as well as for individual subclones.
This study provides simulated genome sequences and whole-exome sequencing reads for artificial bulk tumour samples, as well as for individual subclones. Corresponding mutation profiles are available at https://github.com/GeorgetteTanner/benchmarking.  Genome sequences for individual clones were created using HeteroGenesis (https://github.com/GeorgetteTanner/HeteroGenesis). These were in silico whole-exome sequencing using w-Wessim2 (https://github.com/GeorgetteTanner/w-Wessim2) to create reads for individual clones. Bulk tumour samples were created by merging varying proportions of reads from individual clones, followed by trimming with cutadapt and alignment with BWA mem.   Note that for individual clone fastq files, paired read names end in ".1" and ".2". Some programs may require these to be converted to "/1" and "/2" with "cat {file}.fq | tr '.1' '/1' | tr '.2' '/2' > {out_file}.fq".
This study provides simulated genome sequences and whole-exome sequencing reads for artificial bulk tumour samples, as well as for individual subclones. Corresponding mutation profiles are available at https://github.com/GeorgetteTanner/benchmarking.  Genome sequences for individual clones were created using HeteroGenesis (https://github.com/GeorgetteTanner/HeteroGenesis). These were in silico whole-exome sequencing using w-Wessim2 (https://github.com/GeorgetteTanner/w-Wessim2) to create reads for individual clones. Bulk tumour samples were created by merging varying proportions of reads from individual clones, followed by trimming with cutadapt and alignment with BWA mem.   Note that for individual clone fastq files, paired read names end in ".1" and ".2". Some programs may require these to be converted to "/1" and "/2" with "cat {file}.fq | tr '.1' '/1' | tr '.2' '/2' > {out_file}.fq".