NEWS.md

In DKMS-LSL/dr2s: Dual redundant reference sequencing

DR2S 1.1.16

• [bugfix] fix isues with modified paired-end fastqs by renaming reads after the first mapping and trimming

DR2S 1.1.15

• [bugfix] fix issue with bpparallel in the remapping step that only occurs on the slurm cluster.

DR2S 1.1.14

• [bugfix] fixes multiple issues with parallel access to bam files that only arise on the SLURM cluster.
• [bugfix] depend on dtplyr 1.0.1 for correct handling of .data pronouns.

DR2S 1.1.13

• [bugfix] allow for homozygous samples when downsampling for IGV.

DR2S 0.0.6

• improved identification of highly associated polymorphic positions.
• addition of diagnistic plots plot.mclust.png and plot-mclust.ovl.png.
• minor bugfixes.

DR2S 0.0.5

• implement a JSON-based configuration model and expand configuration options for the individual DR2S pipeline steps.
• add optional read filtering to mapInit() and add "readpicking" plots.
• add optional restriction of partitioning to correlated (i.e., in-phase) SNPs for the lonread-only workflow.
• add correlogram and association plots.
• add a dedicated longread-only pipeline.
• include standard reference data for HLA.
• move from pdf to png for plots.
• cleanup of dependencies.

DR2S 0.0.4

• adapt package for use with a DR2S shiny app.
• create svg plots for use within the shiny app.
• make windows executables for running igv.
• add refineAlignment() to usual reporting workflow.
• refine invocation from config files in yaml format.
• move to cowplot for saving figures.
• Add seqlogo plot.
• Add option to choose between read count and distance for alleles from LR partitioning.
• Add option to prevent clustering by gaps. Useful if only few other SNPs are present.
• Add homopolymer count by mode value.
• Adapt refineAlignment() to cn 1 samples.

DR2S 0.0.3

• Add complete workflow for samples with >2 alleles and 1 allele.
• Add functions to rightshift gaps at homopolymer sites and remove a "backgound gap noise" in Sequel and Nanopore reads.
• Choose clusters by read number.
• Move from hlatools and IPDdata to the new ipd.Hsapiens.db package for creating references.
• Restructure output folder.
• Add executable scripts for IGV and the most useful postprocessing steps.
• Use relative paths so the dr2s object can be read from everywhere.
• Allow fasta files as custom reference.
• Internal code refactoring.

DR2S 0.0.2

• Added a NEWS.md file to track changes to the package.
• Adapt for HLA-A, -B and -C.
• Fill differing short- and long-read length with gaps. Mostly caused by references longer than the sequenced gene.
• More sensitive insert calling.
• Don't allow inserts in the first and last five positions.
• Tested with 3 allele samples.
• Add writing and reading MSA in a phylip-like format.

DKMS-LSL/dr2s documentation built on March 14, 2021, 2:46 p.m.