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GitHub / ajodeh-juma / rvfv-amplicon-seq
A simple pipeline for Rift Valley fever virus consensus genome generation from amplicon sequencing
JSON API: https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ajodeh-juma%2Frvfv-amplicon-seq
Stars: 0
Forks: 0
Open Issues: 0
License: mit
Language: Nextflow
Repo Size: 11.4 MB
Dependencies:
27
Created: almost 2 years ago
Updated: almost 2 years ago
Last pushed: over 1 year ago
Last synced: about 1 year ago
Files
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Dependencies
environment.yml
conda
- bedtools 2.29.2.*
- bioconductor-biostrings 2.58.0.*
- bioconductor-complexheatmap 2.6.2.*
- biopython 1.78.*
- bowtie2 2.4.2.*
- bwa 0.7.17.*
- fastp 0.20.1.*
- fastqc 0.11.9.*
- ivar 1.3.1.*
- multiqc 1.9.*
- nextflow 20.10.0.*
- pandas 1.0.5.*
- picard 2.25.1.*
- r-argparse 2.0.3.*
- r-cowplot 1.1.0.*
- r-data.table 1.13.4.*
- r-ggforce 0.3.3.*
- r-gplots 3.1.1.*
- r-gridextra 2.3.*
- r-hrbrthemes 0.8.0.*
- r-markdown 1.1.*
- r-optparse 1.6.6.*
- r-svglite 1.2.3.2.*
- r-tidyverse 1.3.0.*
- r-viridis 0.5.1.*
- r-zoo 1.8_8.*
- samtools 1.10.*