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Update COVID SC authored by Bruno da Silva Castilho's avatar Bruno da Silva Castilho
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COVID-SC.md
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Pipeline do projeto COVID-SC, criado para identificar novas variantes da COVID-19 no estado.
Pipeline do projeto COVID-SC, criado para identificar novas variantes da COVID-19 no estado. O pipeline tem 18 etapas, conectadas por volumes nfs, onde a saída de uma etapa está conectada na entrada de sua etapa posterior.
#### Links
- [bbmap](https://codigos.ufsc.br/bioinfo/bbmap)
- [bcftools](https://codigos.ufsc.br/bioinfo/bcftools)
- [bwa](https://codigos.ufsc.br/bioinfo/bwa)
- [ivar](https://codigos.ufsc.br/bioinfo/ivar)
- [nextclade](https://codigos.ufsc.br/bioinfo/nextclade)
- [pangolin](https://codigos.ufsc.br/bioinfo/pangolin)
- [python](https://codigos.ufsc.br/bioinfo/python)
- [samtools](https://codigos.ufsc.br/bioinfo/samtools)
- [seqtk](https://codigos.ufsc.br/bioinfo/seqtk)
- [trimmomatic](https://codigos.ufsc.br/bioinfo/trimmomatic)
#### Diagrama do pipeline
![covid-pipeline-docker](uploads/d3da533bdd85e2c95233a1b30a2da956/covid-pipeline-docker.png)
......@@ -210,154 +212,154 @@ volumes:
driver: local
driver_opts:
type: nfs
o: addr=150.162.6.180,rw,async
o: addr=190.162.6.180,rw,async
device: :/export/bioinfo/amostras
reference:
driver: local
driver_opts:
type: nfs
o: addr=150.162.6.180,rw,async
o: addr=190.162.6.180,rw,async
device: :/export/bioinfo/reference
reference_covid:
driver: local
driver_opts:
type: nfs
o: addr=150.162.6.180,rw,async
o: addr=190.162.6.180,rw,async
device: :/export/bioinfo/reference_covid
nextclade_ref_cov:
driver: local
driver_opts:
type: nfs
o: addr=150.162.6.180,rw,async
o: addr=190.162.6.180,rw,async
device: :/export/bioinfo/nextclade_ref_cov
01_prepare_reads:
driver: local
driver_opts:
type: nfs
o: addr=150.162.6.180,rw,async
o: addr=190.162.6.180,rw,async
device: :/export/bioinfo/01_prepare_reads
02_filter_reads_trimmomatic:
driver: local
driver_opts:
type: nfs
o: addr=150.162.6.180,rw,async
o: addr=190.162.6.180,rw,async
device: :/export/bioinfo/02_filter_reads_trimmomatic
03_contamination_bwa_mem:
driver: local
driver_opts:
type: nfs
o: addr=150.162.6.180,rw,async
o: addr=190.162.6.180,rw,async
device: :/export/bioinfo/03_contamination_bwa_mem
04_contamination_samtools_view_sort:
driver: local
driver_opts:
type: nfs
o: addr=150.162.6.180,rw,async
o: addr=190.162.6.180,rw,async
device: :/export/bioinfo/04_contamination_samtools_view_sort
05_contamination_samtools_fastq:
driver: local
driver_opts:
type: nfs
o: addr=150.162.6.180,rw,async
o: addr=190.162.6.180,rw,async
device: :/export/bioinfo/05_contamination_samtools_fastq
06_map_reads_covid_bwa_mem:
driver: local
driver_opts:
type: nfs
o: addr=150.162.6.180,rw,async
o: addr=190.162.6.180,rw,async
device: :/export/bioinfo/06_map_reads_covid_bwa_mem
07_map_reads_covid_samtools_sort:
driver: local
driver_opts:
type: nfs
o: addr=150.162.6.180,rw,async
o: addr=190.162.6.180,rw,async
device: :/export/bioinfo/07_map_reads_covid_samtools_sort
08_statistics_bbmap:
driver: local
driver_opts:
type: nfs
o: addr=150.162.6.180,rw,async
o: addr=190.162.6.180,rw,async
device: :/export/bioinfo/08_statistics_bbmap
09_map_reads_covid_samtools_index:
driver: local
driver_opts:
type: nfs
o: addr=150.162.6.180,rw,async
o: addr=190.162.6.180,rw,async
device: :/export/bioinfo/09_map_reads_covid_samtools_index
10_variant_call_samtools_pileup:
driver: local
driver_opts:
type: nfs
o: addr=150.162.6.180,rw,async
o: addr=190.162.6.180,rw,async
device: :/export/bioinfo/10_variant_call_samtools_pileup
11_variant_call_ivar_variants:
driver: local
driver_opts:
type: nfs
o: addr=150.162.6.180,rw,async
o: addr=190.162.6.180,rw,async
device: :/export/bioinfo/11_variant_call_ivar_variants
12_primers_ivar_trim:
driver: local
driver_opts:
type: nfs
o: addr=150.162.6.180,rw,async
o: addr=190.162.6.180,rw,async
device: :/export/bioinfo/12_primers_ivar_trim
13_assembly_samtools_sort:
driver: local
driver_opts:
type: nfs
o: addr=150.162.6.180,rw,async
o: addr=190.162.6.180,rw,async
device: :/export/bioinfo/13_assembly_samtools_sort
14_assembly_samtools_mpileup:
driver: local
driver_opts:
type: nfs
o: addr=150.162.6.180,rw,async
o: addr=190.162.6.180,rw,async
device: :/export/bioinfo/14_assembly_samtools_mpileup
15_assembly_ivar_consensus:
driver: local
driver_opts:
type: nfs
o: addr=150.162.6.180,rw,async
o: addr=190.162.6.180,rw,async
device: :/export/bioinfo/15_assembly_ivar_consensus
16_concatenate_all_genomes:
driver: local
driver_opts:
type: nfs
o: addr=150.162.6.180,rw,async
o: addr=190.162.6.180,rw,async
device: :/export/bioinfo/16_concatenate_all_genomes
17_annotate_pangolin:
driver: local
driver_opts:
type: nfs
o: addr=150.162.6.180,rw,async
o: addr=190.162.6.180,rw,async
device: :/export/bioinfo/17_annotate_pangolin
18_annotate_nextclade:
driver: local
driver_opts:
type: nfs
o: addr=150.162.6.180,rw,async
o: addr=190.162.6.180,rw,async
device: :/export/bioinfo/18_annotate_nextclade
```
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