Analysis of some of the genes involved in the interaction of Wolbachia and Drosophila, both in restricted and systemic infections
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Klasson's Lab
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Nanopore sequencing
- D. paulistorum O11
- D. paulistorum MS
- D. paulistorum A28
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Illumina sequencing
- D. paulistorum O11
- D. paulistorum MS
- D. paulistorum A28
- D. tropicalis
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RNA Illumina sequencing
- D. paulistorum O11
- D. paulistorum A28
-
-
- Nanopore sequencing
- D. paulistorum L12
- D. paulistorum L06
- D. willistoni LG3
- D. willistoni 00
- D. tropicalis
- D. insularis
- D. sp
- D. sucinea
- Illumina sequencing
- D. paulistorum L06
- D. willistoni LG3
- D. willistoni 00
- D. insularis
- D. sp
- D. sucinea
- Nanopore sequencing
-
- Proteome
- D. melanogaster r6.46 FB2022 03
- D. willistoni r1.3 FB2015 01
- Proteome
Pipeline description and scripts here
- Read preparation
- Whole genome assembly
- Assembly polishing
- Assembly quality evaluation
Pipeline description and scripts here
-
Repeat elements modeler and genome assembly masking
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Gene prediction
- with only Sophophora proteome as evidence
OR
- with Sophophora proteome and RNA seq mapped sequences
Pipeline description and scripts here
- Ortholog finder
- Select genes to study (or all single copy orthologs)
- Keep only longer isoforms
- Gene alignment
- Alignment trimming
- Phylogenetic inference
- Phylogenomic inference
| Software used | version |
|---|---|
| Genome assembly pipeline | |
| Filt-long | 0.2.1 |
| NextDenovo | 2.5.0 |
| Minimap | 2.24 |
| samtools | 1.14 |
| P.E.P.P.E.R-Marign-DeepVariant | 0.4 |
| bcftools | 1.15.1 |
| BWA | 0.7.17 |
| Pilon | 1.24 |
| Gene prediction pipeline | |
| RepeatModeler](https://www.repeatmasker.org/RepeatModeler/) | 1.0.8 |
| BLAST | 2.11.0+ |
| RepeatMasker | 4.0.7 |
| STAR | 2.7.9a |
| Braker | 2.1.6 |
| Ortholog find and phylogenies | |
| OrthoFinder | 2.5.2 |
| MAFFT | 7.407 |
| TrimAl | 1.4.1 |
| IQTREE2 | 2.20 |
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