ngs-4-ecoprod.yml

channels:
  - conda-forge
  - bioconda
  - defaults
  - anaconda
 # - ursky
 # - etetoolkit
dependencies:
  - fastp>=0.23.2
  - fastqc>=v0.11.8
  - parallel>=v20221122
  - cutadapt>=4.2
  - bowtie2>=v2.5.0
  # R
  - r-base>=4.1
  - r-ampvis2>=v2.7.32
  - r-stringr>=v1.3.1
  - r-phytools>=v1.5_1
  - r-viridis>=v0.5.1
  - r-picante>=v1.8.2
  - r-cowplot>=v0.9.3
  - rstudio-desktop>=v2022.12.0
  - rename>=v1.600
  - kraken2>=v2.1.2
  - kaiju>=v1.9.2
  - vsearch>=v2.22.1
  - bioconda::blast
  - fasttree>=v2.1.11
  - mafft>=v7.515
  - porechop_abi>=v0.5.0
  - clustalo>=v1.2.4
  - biopython>=v1.78
  - flye>=v2.9.2
  - medaka>=1.7.2
  - metabat2>=v2.15
  - maxbin2>=v2.2.7
  - semibin>=v1.5.1
  - checkm-genome>=v1.2.2
  - racon>=v1.5.0
  - polypolish>=v0.5.0
  - masurca>=v4.10
  - bwa=>v0.7.17
  - seqtk=>v1.3
  - minimap2=>v2.24
  - bbmap=>v39.01
  - samtools>=v1.17
  - fastani>=v1.33
  - libopenblas>=v0.3.21
  - pydantic>=1.9.2,<2.0a1