software_used.tsv

# base programming language
python=3.7.1
R=3.5.1 

#python packages
# can be installed with pip install --user
snakemake=5.30.1 
pybedtools=0.8.1
pysam=0.16.0.1
pandas=1.1.3
flask=1.1.2
graphviz=0.14.2
PyPDF2=1.26.0
markdown=3.0.1
weasyprint=51

# R libraries
# can be installed with install.packages() function in R
tidyverse=1.2.1
magrittr=1.5
ape=5.4.1
edgeR=3.24.3
optparse=1.6.2

# Bioinformatic softwares
# manual install
minigraph=0.12-r389 
gfatools=0.4-r179-dirty

# available in bioconda 
gatk4=4.1.9.0
samtools=1.10
bedtools=2.29.0
seqkit=0.15.0
graphaligner=1.0.12 
mash=2.2
RepeatMasker=4.1.1
diamond=0.9.30.131
hisat2=2.1.0
augustus=3.3.3
stringtie=2.1.1
graphviz
vt=0.5
bcftools=1.8
bwa=0.7.17-r1188
samblaster=0.1.24
fastp=0.19.4