Doc_ID:
Editor: Angela
Reviewer:
| Software | Conda command | Version | Remark |
| bowtie | conda install bowtie | bowtie=1.2.3 | |
| bowtie2 | conda install bowtie2 | bowtie2=2.4.1 | |
| bwa | conda install bwa | bwa=0.7.17 | |
| bcftools | conda install -c bioconda bcftools | bcftools=1.10.2 | |
| bedtools | conda install bedtools | bedtools=2.29.2 | |
| cnvkit | conda install cnvkit | cnvkit=0.9.7 | |
| delly | conda install delly | delly=0.8.3 | |
| edger | conda install -c bioconda bioconductor-edger | edger=3.30.0 | |
| fastp | conda install fastp | fastp=0.20.1 | |
| fastqc | conda install fastqc | fastqc=0.11.9 | |
| gatk4 | conda install gatk4 | gatk4=4.1.8.1 | |
| igv | conda install -c bioconda igv | igv=2.4.9 | |
| multiqc | conda install multiqc | multiqc=1.9 | |
| picard | conda install picard | picard=2.23.4 | |
| hisat2 | conda install hisat2 | hisat2=2.2.1 | |
| qualimap | conda install qualimap | qualimap=2.2.2d | |
| rclone | conda install -c conda-forge rclone | rclone=1.52.3 | |
| rsem | conda install rsem | rsem=1.3.3 | |
| sratoolkit | conda install -c daler sratoolkit | sratoolkit=2.5.7 | |
| r-monocle3 | conda install -c bioconda r-monocle3 | r-monocle3=0.2.2 | |
| r-seurat | conda install -c bioconda r-seurat | r-seurat=3.2.1 | |
| deseq2 | conda install -c bioconda bioconductor-deseq2 | bioconductor-deseq2=1.28.0 | |
| sambamba | conda install sambamba | sambamba=0.7.1 | |
| samtools | conda install samtools | samtools=1.10 | |
| sratoolkit | conda install rsem | rsem1.3.3 | |
| star | conda install star | star=2.7.5a | |
| stringtie | conda install stringtie | stringtie=2.1.2 | |
| trimmomatic | conda install trimmomatic | trimmomatic=0.39 | |
| trinity | conda install trinity | trinity=2.9.1 |