Repository containing commands and scripts to generate the genome assemblies and perform the comparative genomics analyses. The genome sequence of Gr-Line19 is available under BioSample: SAMN17613196 and the genome sequence of Gr-Line22 is available under BioSample: SAMN17613218
The sequence reads used in this project are available at the NCBI SRA database under BioProject PRJNA695196
| NCBI SRA ID | Spots | Platform | Isolate |
|---|---|---|---|
| SRR13560389 | 23668331 | ILLUMINA | Gr-Line19 |
| SRR13560388 | 23544408 | ILLUMINA | Gr-Line19 |
| SRR13560391 | 23579544 | ILLUMINA | Gr-Line22 |
| SRR13560390 | 23640685 | ILLUMINA | Gr-Line22 |
| SRR13560397 | 653296 | PACBIO_SMRT | Gr-Line19 |
| SRR13560396 | 648034 | PACBIO_SMRT | Gr-Line19 |
| SRR13560395 | 701627 | PACBIO_SMRT | Gr-Line19 |
| SRR13560394 | 603883 | PACBIO_SMRT | Gr-Line22 |
| SRR13560393 | 508886 | PACBIO_SMRT | Gr-Line22 |
| SRR13560392 | 560230 | PACBIO_SMRT | Gr-Line22 |
The detailed pipeline description with the exact commands used is explained in Assembly/Pipeline.md. Various custom scripts used in the pipeline are available in the folder Assembly/
Gene predictions were done as described in BRAKER_grene_predictions.md
Masking of repeats is done through RepeatModeler/Repeatmasker using a custom pipeline that is available here: https://github.com/Jorisvansteenbrugge/RepeatMaskPipeline. The pipeline was run with the following commands:
$ mkdir gr19_repeatmask
$ mkdir gr22_repeatmask
$ Repeatmask_pipeline run all --workdir gr19_repeatmask/ -i G_rostochiensis_v10_L19_named.fasta -p 8
$ Repeatmask_pipeline run all --workdir gr22_repeatmask/ -i G_rostochiensis_v10_L22_named.fasta -p 8