We have a lot of software already installed on the server that covers applications ranging from QC analysis and preprocessing of raw sequence data, transcriptome analysis from RNAseq data, 16S and shotgun metagenomics pipelines, WGS tools, and more. If you have an account on our cluster, then you already have access to all of the software below, so get started!
If you’re looking for a piece of software and don’t find it below, just reach out to Dan Beiting to inquire about getting it installed.
NOTE: When available, I’ve included the appropriate publication/reference for each piece of software. Please cite the authors if you use their software! if a piece of software has not been published, you should cite the github repo or software website
| software | Version | Website | Citation | category | how to run | When to use | Reference files or databases | |
|---|---|---|---|---|---|---|---|---|
anvi’o | 7.1 | metagenomicsvisualizationMAGs | conda activate anvio-7.1 | When you're ready to dive into Metagenome Assembled Genomes (MAGs). | ||||
Amazon Web Services Command Line Interface (AWS CLI) | 2.12.6 | unpublished | utility | aws | When you want to get reference genomes from the Illumina iGenomes project: https://ewels.github.io/AWS-iGenomes/ | |||
1.5.3 | unpublished | NGS tools | bs | |||||
bcftools | 1.18 | NGS tools | conda activate bcftools then bcftools | |||||
bcl2fastq | v2.19.0.316 | unpublished | NGS tools | conda activate bcl2fastq | ||||
2.31.0 | NGS tools | bedtools | Anytime you want to calculate genomic metrics from sequence data (e.g. coverage) | |||||
BLAST | 2.12.0 | sequence search | blastn, blastp, or blastx | |||||
2.5.1 | read alignmentMicrobial ecology pipeline for 16S rRNA data | bowtie2 | One of the best and most popular base-wise aligners. Even if you don't use it as your primary aligner, it is still used by many other software tools under the hood. | prebuilt bowtie2 indexes for many species are located in /data/reference_db in folders named by genus and species | ||||
0.7.17-r1188 | read alignment | bwa | I don't use this directly, but used by other programs for alignment | |||||
CellxGene gateway | 0.3.11 | unpublished | single cell | cellxgene-gateway | Allows us to host a cellxgene instance that works with multiple datasets | /data/reference_db/cellxgene_data | ||
CellRanger | 7.1.0 | single cell | cellranger | If you want to preprocess single cell genomic data from the 10x platform | ||||
CellRanger-arc | 2.0.2 | single cell | cellranger-arc | If you want to preprocess single cell genomic data from the 10x platform | ||||
1.1.3 | metagenomicsgenome assemblyQA/QC | conda activate checkm then checkm lineage_wf | If you have a bacterial genome assembly and want to check the quality of the assembly | /data/reference_db/checkm | ||||
1.18.0 | transcriptomics | clust | If you have an RNAseq dataset with multiple timepoints and want to identify 'tight' modules of co-regulated genes across these timepoints. Clust also allows comparison of modules between datasets/experiments. | |||||
3.5.2 | visualizationNGS tools | deeptools | ||||||
2.1.8 | multiple sequence alignment | diamond | If you have a bunch of protein AA or translated DNA sequences that you want to align. | diamond formatted databases for UniRef90 and UniRef50 live in /data/reference_db/uniref | ||||
Docker | 24.0.2, build cb74dfc | unpublished | containerized software | docker run [OPTIONS] IMAGE [COMMAND] [ARG...] | ||||
Dorado | 0.3.1+bb8c5ee | unpublished | nanoporebasecallingGPU | dorado | ||||
0.23.4 | QA/QC | fastp | ||||||
0.12.1 | unpublished | QA/QC | fastqc | The preferred choice for rapid quality control assessment of raw reads in a fastq file | ||||
0.15.3 | decontaminationQA/QC | fastq_screen | simple tool for figuring out if you fastq file has 'contaminating' reads from specific species. uses bowtie2 under the hood. | |||||
Filezilla | 3.63.0 | unpublished | utility | filezilla | ||||
0.2.1 | unpublished | QA/QCnanopore | filtlong | If you have Oxford Nanopore long read data and want to filter your raw data to remove reads based on length or quality | ||||
1.3.6 | variantsSNPs/INDELs | freebayes | For variant calling | |||||
4.4.0.0 | variants | gatk | When you are working with SNPs/variants | |||||
0.7.0 | public data | grabseqs | A convenient wrapper around the fasterq_dump software that makes it easy to grab sequences from SRA, ENA, MGRAST and iMicrobe | |||||
GTDB-TK | 2.1.1 | metagenomicsclassification | conda activate gtdb may need to run export GTDBTK_DATA_PATH=/data/reference_db/GTDB-Tk/release214 to make sure your environment ‘sees’ the reference database | /data/reference_db/GTDB-Tk | ||||
3.7 | metagenomicsfunctional profiling | You have shotgun metagenomic data from a microbial community and want to understand functional content (e.g. bacterial metabolic pathways). Note that humann2 uses DIAMOND, MinPath and Bowtie2 under the hood | ||||||
htop | 3.2.2 | unpublished | utility | htop | ||||
1.10 | metagenomics | iRep or bPTR | ||||||
2.3.1 | NGS tools | jellyfish | For rapid/efficient counting of kmers in DNA | |||||
0.50.1 | transcriptomicsread alignment | kallisto | Our preferred choice for mapping RNA-seq raw reads to a reference transcriptome | prebuilt kallisto indexes for a few species in /data/reference_db/kallisto | ||||
0.27.3 | single cell | kb | A great alternative to CellRanger for preprocessing single cell data from the 10x platform. | prebuilt kallisto indexes for a few species in /data/reference_db/kallisto | ||||
0.12.0 | unpublished | decontamination | kneaddata | If you want to remove 'contaminating' reads from a fastq file. Uses bowtie2 under the hood | ||||
2.0.7-beta | metagenomicsclassification | conda activate kraken thenkraken2 | /data/reference_db/kraken2db_standard/ | |||||
Krakenuniq | 0.5.8 | metagenomicsclassification | conda activate kraken thenkrakenuniq | |||||
3.0.0a6 | Epigenetics | conda activate macs3 then macs3 | Anytime you have ATAC-seq or ChIP-seq data and want to identify 'peaks' or read pile-ups at specific positions in the genome | |||||
marker_alignments | 0.4.2 | metagenomicsclassification | marker_alignments | If you want to find microbial eukaryotes in metagenomic data | the EukDetect database used by this program lives in /data/reference_db/eukdetect | |||
Mastiff | 0.0.3 | unpublished | metagenomicspublic data | mastiff | ||||
MaxBin2 | 2.2.7 | assembly | run_MaxBin.pl | |||||
1.2.9 | assemblymetagenomics | megahit | If you want to assemble genomes from metagenomic data | |||||
4.06 | metagenomicsclassification | conda activate biobakery and then metaphlan | /data/reference_db/biobakery | |||||
Micro | 2.0.11 | unpublished | utility | micro | anytime you need to edit a text file in the terminal….it’s far better than vim or nano! | |||
0.3.4 | NGS tools | mosdepth and plot-dist.py for plotting | ||||||
1.14 | unpublished | QA/QC | multiqc | Our preferred choice for quickly and easily summarizing QC metrics, as well as outputs from MANY other programs, in a convenient html report | ||||
23.04.2.5870 | unpublished | workflow management | nextflow | If you want to set up an automated workflow on our server | ||||
nf-core | 2.10 | workflow management | nf-core | |||||
nvitop | 1.1.2 | unpublished | utilityGPU | pipx run nvitop | ||||
nvtop | 3.0.1 | unpublished | utilityGPU | nvtop | ||||
3.0.0 | unpublished | NGS tools | java -jar /usr/local/bin/picard.jar | One of the main places we use this is for filtering out PCR duplicates in our ATAC-seq workflow | ||||
1.07 | comparative genomics | plink | Used for GWAS and other popgen analyses | |||||
0.2.4 (no longer maintained/supported) | unpublished | QA/QCnanopore | porechop | When you have Nanopore reads and you want to trim off the adapter sequence | ||||
1.14.6 | annotation | prokka | Great for quickly (and accurately) annotating a bacterial genome | |||||
2023.5.1 | 16S | source activate qiime2-2023.5 and then qiime | Anytime you want to figure out microbial community composition from 16S data | |||||
1.9.1 | 16S | source activate qiime1 and then qiime | ||||||
Rosella | 0.4.2 | unpublished | metagenomicsbinningMAGs | |||||
rust | 1.26.0 | programming language | rustup or cargo or rustc | |||||
1.16.1 | NGS tools | samtools | A powerful suite of tools for working with aligment files (bam, sam, etc) | |||||
1.3-r106 | working with fasta/fastq | seqtk | I use this anytime I want to quickly subsample a fastq file | |||||
2.3.0 | working with fasta/fastq | seqkit | Anytime you need to manipulate a fastq/a file. Some overlap in functionality with seqtk | |||||
5.1d | unpublished | SNPs/INDELs | java -jar /usr/local/bin/snpEff/snpEff.jar for snpEff and java -jar /usr/local/bin/snpEff/SnpSift.jar for snpSift | |||||
3.15.4 | assemblymetagenomics | spades.py [options] -o <output_dir> | If you have a metagenomic sequencing data and want to assemble microbial genomes de novo | |||||
SWGA2 | 1.0.0 | metagenomics | conda activate swga2 then soapswga | when you want to design primers for carrying out selective whole genome amplification (SWGA) | ||||
4.8.2 | metagenomicsclassification | sourmash | Fantastic software that takes an alignment-free approach to compare two or more fastq files to each other, or to all of refseq or genbank to understand what organisms might be present in the data. | |||||
3.0.5 | public data | fasterq_dump, sam-dump, and more | ||||||
2.7.10b | read alignment | STAR (all caps) or STARlong (for aligning long reads) | Very fast and popular base-wise aligner | prebuilt STAR indexes for several species present in /data/reference_db/star | ||||
StrainPhlAn | 4.0.6 | metagenomicsclassification | conda activate biobakery and then strainphlan | |||||
4.1.0 | metagenomicsclassification | conda activate sunbeam4.1.0 | ||||||
0.39 | QA/QC | java -jar /usr/local/bin/Trimmomatic/trimmomatic-0.39.jar | Anytime you need to trim or filter raw reads from a fastq file based on base quality scores or length | |||||
0.5.0 | assembly | unicycler | If you have short (Illuminati) and long (Nanopore or PacBio) reads from a bacterial isolate and want to get a complete genome assembly | |||||
VCFtools | 0.1.17 | variants | vcftools | |||||
velocyto | 0.17 | single cell | veloctyo | |||||