chiamh

Primer3-py 2.3.0 and bbmap 39.52

Blast 2.12.0

https://github.com/beliveau-lab/OligoMiner and seqkit 2.3.0

Bedtools, picard, seqkit and bbmap

For downloading species fasta/gffs. r-base 4.43, tidyverse 2.0.0, biomartr 1.0.7, stringr 1.6.0

Conda environment for vsearch v2.30.1

Contains umi_tools v 1.1.5

Contains vg 1.63.1 (pangenome mapper) and seqtk 1.3

Contains samtools 1.13 and seqtk 1.2-r94

Conda image of stereopy v 1.3.1

samtools 1.3.1, bwa 0.7.17, fastp 0.22.0, pysam 0.19.1

Microbeannotator v 2.0.5 (https://github.com/cruizperez/MicrobeAnnotator)

awscli v 1.25.7

Conda environment for salmon v 1.10.1

Eggnog mapper2.1.6, bbmap 38.93 & bedtools2.3.0

bowtie2.4.4, bbmap38.93 & samtools1.13

For metagenomics and metatranscriptomics pipeline building.