Bioinformatics Software
A lot of Bioinformatics software can now be installed via Anaconda Python. These packages can be accessed on all MCSR systems by loading the main Python module and loading the bioinf
environment. These packages are listed below. All other Bioinformatics software is listed on the main documentation page.
To use the bioinf
environment:
module load python
source activate bioinf
The packages installed in the bioinf
environment include:
- ALE
- ARAGORN
- Bandage
- bcftools
- BioPerl
- BLAST
- bowtie2
- Canu
- cd-hit
- CheckM
- Deepbinner
- DeepBGC
- EMBOSS
- FastANI
- FGMP
- Filtlong
- FMLRC
- freebayes
- GMAP/GSNAP
- HMMER
- htseq
- iqtree
- MetaBGC
- MetaPhlAn2
- mothur
- MUMmer
- MUSCLE
- MultiQC
- NumPy
- PANDAS
- Prodigal
- Prokka
- RAxML
- SAMtools
- SciPy
- Sickle
- SPAdes
- VSEARCH