DEST: Drosophila Evolution over Space and Time

Version 2 (2023)

Scripts and tools for mapping and quality control of DEST dataset

Citations (public releases)

Version 2:

Version 1: https://doi.org/10.1093/molbev/msab259

General Pipeline, Map to Hologenome w/ BWA-MEM

graph LR
2[Single End] -->  4[Prep+Merge] 
3[Pair End] -->  5[Prep] 
4[Prep]  --BWA-MEM--> 8[merged+unmerged] --> 10[Merge+Sort Sam]
5[Prep]  --BWA-MEM--> 9[single end] --> 11[SortSam]

10[Merge+Sort Sam] --> 12[Remove Duplicates]
11[SortSam] --> 12[PICARD MarkDuplicate]

12[Remove Duplicates] --> 13[GATK-indel corr.]

13[GATK-indel corr.] --> 14(BAM)

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Species Specific Pipeline

graph LR
14(BAM) --> 15{Species filter} 
15{Species filter} --> 16[Melanogaster]
15{Species filter} --> 17[Simulans] --> 18[Assess Contamination]
16[Melanogaster] --> 19[Mpileup] --> 20[Sync]
19[Mpileup] --> 21[SNAPE filters Sync]

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Changes in Version 2.0 (Spring 2023)

• The DEST docker pipeline can now map both single-end and pair-end reads. Previously, only paired-end reads were available
• New naming convention: samples in version 2 have new names. These names are now in the form: "CH_Fri_Ors_1_2020-08-23". These fields represent "Country Code" _ "region code" _ "city code" _ "replicate code" _ "year" _ "month" _ "date". This replaces the old nomenclature. A conversion table is now available in the metadata file.

Metadata

populationInfo\: Has supplemental data from the DrosEU, DrosRTEC, and DPGP files to make a unified meta-datafile. This datafile is supplemental table 1 of Kapun et al 2021. The meta-data file includes collection information, library quality filtering, inversion frequencies, weather stations and WorldClim environmental data.

PoolSeq mapping pipeline

mappingPipeline\: Contains dockerized mapping pipeline. Downloads data, produces bam files, filter files, gSYNC files

Incorporate Drosophila Genome Nexus data

add_DGN_datda\: Downloads, formats, lifts-over the Drosophila Genome Nexus data into gSYNC format

SNP calling

snpCalling\: SNP calling based on gSYNC files. Runs PoolSNP and SNAPE using snakemake pipeline

Example Scripts

examples: Provides a basic script to pull allele frequencies from a GDS table and also calculates the effective coverage