Appendix V - Bioinformatic pipelines/scripts
收藏DataCite Commons2020-08-25 更新2025-04-17 收录
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https://leicester.figshare.com/articles/Appendix_V_-_Bioinformatic_pipelines_scripts/12363785/1
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PhD thesis: PRDM9 Diversity, Recombination Landscapes and Childhood Leukaemia by Ihthisham Ali <br><br>Appendix V contains various data pipelines and scripts used for the remapping of Illumina HiSeq2000 dataset to known PRDM9 ZnF arrays, read depth and variant calling vcf file generation, haplotype estimation and imputation of FIGNL1 coding variants in relation to the British ALL cohort, de novo assembly of read data and mapping of MinION read data.<br>A. ALL study phasing and imputationB. Illumina HiSeq 2000 dataset - Read depth (DP) and variant calling pipelineC. Illumina HiSeq 2000 dataset - data treatmentD. VelvetOptimiser best k-mer determination log (exemplary)E. Alignment of contigs generated by Velvet de novo assembly for the PRDM9 A/A carrier and aligned against the PRDM9 A ZnF arrayF. MinION nanopore reads - minimap2 pipeline
提供机构：
University of Leicester
创建时间：
2020-06-02
