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--- detection_of_recombination_in_bacterial_genomes [2018/06/18 08:12] – [Gubbins] hyjeong
+++ detection_of_recombination_in_bacterial_genomes [2021/03/17 13:09] (current) – external edit 127.0.0.1
@@ Line 30: / Line 30: @@
 /data/anaconda2/bin/freebayes-parallel의 40번째 라인을 찾아가서 위 두 가지 유틸리티 앞에 붙은 상대경로를 지워버렸다. 이렇게 하니 비로소 정상적인 실행이 되었다. 일반적인 실행 방법은 다음과 같다.
-  $ snippy --cpus 16 outdir mysnps --ref E_coli.gbk --R1 read_1.fastq.gz --R2 read_2.fastq.gz
+  $ snippy --cpus 16 --outdir mysnps --ref E_coli.gbk --R1 read_1.fastq.gz --R2 read_2.fastq.gz
   $ snippy-core --prefix core mysnps1 mysnps2 mysnps2
 snippy-core 결과물인 core.full.aln(whole genome SNP alignment including invariant sites)을 gubbins에 이용하면 된다.
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   * [논문] Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucl Acid Res 2015 [[https://www.ncbi.nlm.nih.gov/pubmed/25414349|PubMed]]
   * [[https://www.sanger.ac.uk/science/tools/gubbinshttps://www.sanger.ac.uk/science/tools/gubbins|웹사이트]] [[https://github.com/sanger-pathogens/gubbins|GitHub]]
+BioConda 패키지를 이용하여 설치하였다(py35 environment).
+  $ run_gubbins.py dataset.aln
+  $ gubbins_drawer.py -o result.pdf dataset.final_tree.tre dataset.recombination_predictions.embl
+  $ gubbins_drawer.py -o results_SNPS.pdf dataset.final_tree.tre dataset.branch_base_reconstruction.embl
 ===== Visualization using phandango =====