Software we use

8.0

Community-led, integrated, reproducible multi-omics with anvi’o and Anvi’o: an advanced analysis and visualization platform for ‘omics data

conda activate anvio-7.1

When you're ready to dive into Metagenome Assembled Genomes (MAGs).

2.12.6

unpublished

aws

When you want to get reference genomes from the Illumina iGenomes project: https://ewels.github.io/AWS-iGenomes/

1.5.3

unpublished

bs

1.18

Twelve years of SAMtools and BCFtools

conda activate bcftools then bcftools

2.20.0.422

unpublished

bcl2fastq -R $rundirectory -o $outdirectory --sample-sheet $samplesheet.csv --no-lane-splitting

4.2.7

unpublished

bcl-convert

2.31.0

BEDTools: a flexible suite of utilities for comparing genomic features

bedtools

Anytime you want to calculate genomic metrics from sequence data (e.g. coverage)

2.12.0

Basic Local Alignment Search Tool

blastn, blastp, or blastx

2.5.1

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome and Fast gapped-read alignment with Bowtie2

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

Fast and accurate short read alignment with Burrows–Wheeler transform

bwa

I don't use this directly, but used by other programs for alignment

0.3.11

unpublished

cellxgene-gateway

Allows us to host a cellxgene instance that works with multiple datasets

/data/reference_db/cellxgene_data

9

cellranger

If you want to preprocess single cell genomic data from the 10x platform

2.0.2

cellranger-arc

If you want to preprocess single cell genomic data from the 10x platform

1.1.3

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

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

Clust: automatic extraction of optimal co-expressed gene clusters from gene expression data

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

deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis

deeptools

2.1.8

Fast and sensitive protein alignment using DIAMOND

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

24.0.2, build cb74dfc

unpublished

docker run [OPTIONS] IMAGE [COMMAND] [ARG...]

1.1.1

unpublished

dorado

0.23.4

fastp: an ultra-fast all-in-one FASTQ preprocessor

fastp

0.12.1

unpublished

fastqc

The preferred choice for rapid quality control assessment of raw reads in a fastq file

0.15.3

FastQ Screen: A tool for multi-genome mapping and quality control

fastq_screen

simple tool for figuring out if you fastq file has 'contaminating' reads from specific species. uses bowtie2 under the hood.

3.63.0

unpublished

filezilla

0.2.1

unpublished

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

Haplotype-based variant detection from short-read sequencing

freebayes

For variant calling

4.6.2

gatk

When you are working with SNPs/variants

0.7.0

grabseqs: simple downloading of reads and metadata from multiple next-generation sequencing data repositories

grabseqs

A convenient wrapper around the fasterq_dump software that makes it easy to grab sequences from SRA, ENA, MGRAST and iMicrobe

2.1.1

GTDB-Tk2: memory friendly classification with the genome taxonomy database and GTDB-Tk: A toolkit to classify genomes with the Genome Taxonomy Database

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

Species-level functional profiling of metagenomes and metatranscriptomes

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

Humann: How to Set up / Run on Paired Files

3.2.2

unpublished

htop

1.10

Measurement of bacterial replication rates in microbial communities

iRep or bPTR

2.3.1

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

jellyfish

For rapid/efficient counting of kmers in DNA

0.50.1

Near-optimal probabilistic RNA-seq quantification

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

Near-optimal probabilistic RNA-seq quantification and Modular, efficient and constant-memory single-cell RNA-seq preprocessing

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

kneaddata

If you want to remove 'contaminating' reads from a fastq file. Uses bowtie2 under the hood

2.0.7-beta

Kraken: ultrafast metagenomic sequence classification using exact alignments and Improved metagenomic analysis with Kraken 2

conda activate kraken thenkraken2

/data/reference_db/kraken2db_standard/

0.5.8

KrakenUniq: confident and fast metagenomics classification using unique k-mer counts

conda activate kraken thenkrakenuniq

3.0.0a6

Model-based Analysis of ChIP-Seq (MACS) and Improved peak-calling with MACS2

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

0.4.2

Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes

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

0.0.3

unpublished

mastiff

2.2.7

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

run_MaxBin.pl

1.2.9

An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph and A Fast and Scalable Metagenome Assembler driven by Advanced Methodologies and Community Practices

megahit

If you want to assemble genomes from metagenomic data

4.06

Metagenomic microbial community profiling using unique clade-specific marker genes and Extending and improving metagenomic taxonomic profiling with uncharacterized species with MetaPhlAn 4

conda activate biobakery and then metaphlan

/data/reference_db/biobakery

2.0.11

unpublished

micro

anytime you need to edit a text file in the terminal….it’s far better than vim or nano!

0.3.4

Mosdepth: quick coverage calculation for genomes and exomes

mosdepth and plot-dist.py for plotting

1.14

unpublished

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

nextflow

If you want to set up an automated workflow on our server

2.10

The nf-core framework for community-curated bioinformatics pipelines

nf-core

1.1.2

unpublished

pipx run nvitop

3.0.1

unpublished

nvtop

3.0.0

unpublished

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

Second-generation PLINK: rising to the challenge of larger and richer datasets

plink

Used for GWAS and other popgen analyses

0.2.4 (no longer maintained/supported)

unpublished

porechop

When you have Nanopore reads and you want to trim off the adapter sequence

1.14.6

Prokka: rapid prokaryotic genome annotation

prokka

Great for quickly (and accurately) annotating a bacterial genome

2023.5.1

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

source activate qiime2-2023.5 and then qiime

Anytime you want to figure out microbial community composition from 16S data

1.9.1

QIIME allows analysis of high-throughput community sequencing data

source activate qiime1 and then qiime

0.4.2

unpublished

1.26.0

rustup or cargo or rustc

1.16.1

The Sequence Alignment/Map format and SAMtools

samtools

A powerful suite of tools for working with aligment files (bam, sam, etc)

1.3-r106

seqtk

I use this anytime I want to quickly subsample a fastq file

2.3.0

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

seqkit

Anytime you need to manipulate a fastq/a file. Some overlap in functionality with seqtk

5.1d

unpublished

java -jar /usr/local/bin/snpEff/snpEff.jar for snpEff and java -jar /usr/local/bin/snpEff/SnpSift.jar for snpSift

3.15.4

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

spades.py [options] -o <output_dir>

If you have a metagenomic sequencing data and want to assemble microbial genomes de novo

1.0.0

A fast machine-learning-guided primer design pipeline for selective whole genome amplification

conda activate swga2 then soapswga

when you want to design primers for carrying out selective whole genome amplification (SWGA)

4.8.2

sourmash: a library for MinHash sketching of DNA

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.

2.1.1

unpublished

spaceranger

When you have spatial gene expression from the Visium 10x platform

3.0.5

fasterq_dump, sam-dump, and more

2.7.10b

STAR: Ultrafast Universal RNA-seq Aligner

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

4.0.6

Microbial strain-level population structure and genetic diversity from metagenomes

conda activate biobakery and then strainphlan

4.1.0

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments

conda activate sunbeam4.1.0

Sunbeam: How to Set-up / Run

0.39

Trimmomatic: a flexible trimmer for Illumina sequence data

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

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

unicycler

If you have short (Illuminati) and long (Nanopore or PacBio) reads from a bacterial isolate and want to get a complete genome assembly

0.1.17

vcftools

0.17

RNA velocity of single cells

veloctyo

0.5.2

Latest one stop bacterial genome assembler from Unicycler authors