List of software and uses

software	Version	Website	Citation	category	how to run	When to use	Reference files or databases
anvi’o	7.0	merenlab.org	Community-led, integrated, reproducible multi-omics with anvi’o and Anvi’o: an advanced analysis and visualization platform for ‘omics data	metagenomicsvisualization	`source activate anvio-7`	When you're ready to dive into Metagenome Assembled Genomes (MAGs).
BamM	1.7.3	ecogenomics.github.io	unpublished	NGS tools	`bamm`
Bandage	NA	rrwick.github.io	Bandage: interactive visualization of de novo genome assemblies	genome assembly visualization	`Bandage` (must be sitting at the Linux to use, since it is a graphical interface)
BaseSpace Sequence Hub CLI tool suite	1.1.0	developer.basespace.illumina.com	unpublished	NGS tools	`bs`
bcftools		samtools.github.io		NGS tools	`bcftools`
bedtools	2.26.0	bedtools.readthedocs.io	BEDTools: a flexible suite of utilities for comparing genomic features	NGS tools	`bedtools`	Anytime you want to calculate genomic metrics from sequence data (e.g. coverage)
BLAST	2.9.0	blast.ncbi.nlm.nih.gov	Basic Local Alignment Search Tool	sequence search	option include `blastn`, `blastp`, or `blastx`
bowtie2	2.3.4.1	bowtie-bio.sourceforge.net	Ultrafast and memory-efficient alignment of short DNA sequences to the human genome and Fast gapped-read alignment with Bowtie2	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
BWA	0.7.17-r1188	bio-bwa.sourceforge.net	Fast and accurate short read alignment with Burrows–Wheeler transform	read alignment	`bwa`	I don't use this directly, but used by other programs for alignment
CellRanger	7.0.0	support.10xgenomics.com		single cell	`cellranger`	If you want to preprocess single cell genomic data from the 10x platform
CellRanger-arc	2.0.1	support.10xgenomics.com		single cell	`cellranger-arc`	If you want to preprocess single cell genomic data from the 10x platform
Circos		circos.ca		visualization	circos
CheckM	1.1.3	ecogenomics.github.io	CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes	metagenomicsgenome assemblyQA/QC	`checkm lineage_wf`	If you have a bacterial genome assembly and want to check the quality of the assembly	uses checkm_db, which is located in /data/reference_db
Clust	1.17.0	github.com	Clust: automatic extraction of optimal co-expressed gene clusters from gene expression data	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.
CONCOCT	1.1.0	concoct.readthedocs.io	Binning metagenomic contigs by coverage and composition	metagenomics	`concoct`	When you have metagenomic data and want to put de novo assembled contigs into genome bins
Cytoscape		cytoscape.org		network analysis	navigate to /home/shared/softwares/Cytoscape_v3.5.1 folder. Double click to open program
deeptools	3.5.1	deeptools.readthedocs.io	deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis	visualizationNGS tools	`deeptools`
DESMAN		github.com	DESMAN: a new tool for de novo extraction of strains from metagenomes	metagenomics	`desman`	If you want to identify strains in your metagenomic data
DIAMOND	0.8.22.84	www.diamondsearch.org	Fast and sensitive protein alignment using DIAMOND	multiple sequence alignment	`diamond`	If you have a bunch of protein AA or translated DNA sequences that you want to align.
EMIRGE		github.com	Reconstruction of full-length ribosomal genes from microbial community short read sequencing data and Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments	metagenomics16S	`emirge.py` or `emirge_amplicon.py`
Fastp	0.20.1	github.com	fastp: an ultra-fast all-in-one FASTQ preprocessor	QA/QC	`fastp`
FastQC	0.11.7	www.bioinformatics.babraham.ac.uk	unpublished	QA/QC	`fastqc`	The preferred choice for rapid quality control assessment of raw reads in a fastq file
FastQ Screen	0.15.1	www.bioinformatics.babraham.ac.uk	FastQ Screen: A tool for multi-genome mapping and quality control	decontamination	`fastq_screen`	simple tool for figuring out if you fastq file has 'contaminating' reads from specific species. uses bowtie2 under the hood.
Filtlong	0.2.0	github.com	unpublished	QA/QC	`filtlong`	If you have Oxford Nanopore long read data and want to filter your raw data to remove reads based on length or quality
Freebayes	1.3.6	github.com	Haplotype-based variant detection from short-read sequencing	variantsSNPs/INDELs	`freebayes`	For variant calling
GATK	4.1.7.0	gatk.broadinstitute.org		variants	`gatk`	When you are working with SNPs/variants
Grabseqs	0.7.0	github.com	grabseqs: simple downloading of reads and metadata from multiple next-generation sequencing data repositories	public data	`grabseqs`	A convenient wrapper around the fasterq_dump software that makes it easy to grab sequences from SRA, ENA, MGRAST and iMicrobe
GraPhlAn	1.1.3	huttenhower.sph.harvard.edu	Compact graphical representation of phylogenetic data and metadata with GraPhlAn	metagenomics visualization	`graphlan.py` or `graphlan_annotate.py`	If you want to create a visual link between microbiome samples, their phylogenetic relationship and sample or patient metadata
GroopM	0.3.4	ecogenomics.github.io	GroopM: an automated tool for the recovery of population genomes from related metagenomes	metagenomics	`groopm`
HISAT2		daehwankimlab.github.io	Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
Humann3	3.0.0.alpha.2	huttenhower.sph.harvard.edu	Species-level functional profiling of metagenomes and metatranscriptomes	metagenomics	`humann2`	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
HTSeq	0.13.5	htseq.readthedocs.io	HTSeq — A Python framework to work with high-throughput sequencing data	transcriptomics	`htseq-count` or `htseq-qa`	If you’ve already aligned data using a base-aware aligned (e.g. STAR or Bowtie2) and you want to summarize reads to genomic features (genes, exons, etc)
iRep	1.1.14	github.com	Measurement of bacterial replication rates in microbial communities	metagenomics	`iRep` or `bPTR`
Kallisto	0.46.0	pachterlab.github.io	Near-optimal probabilistic RNA-seq quantification	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
Kallisto-BUStools	0.27.3	www.kallistobus.tools	Near-optimal probabilistic RNA-seq quantification and Modular, efficient and constant-memory single-cell RNA-seq preprocessing	single cell	`conda activate kb` then `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
KneadData	0.6.1	huttenhower.sph.harvard.edu	unpublished	decontamination	`kneaddata`	If you want to remove 'contaminating' reads from a fastq file. Uses bowtie2 under the hood
MinPath		omics.informatics.indiana.edu	A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes	biological pathway reconstructions using protein family predictions	MinPath1.4.py
Kraken2	2.0.6 beta	ccb.jhu.edu	Kraken: ultrafast metagenomic sequence classification using exact alignments and Improved metagenomic analysis with Kraken 2	metagenomics	`kraken2`		kracken reference database is in /data/reference_db/kraken2db_standard/
MACS3	3.0.0a6	macs3-project.github.io	Model-based Analysis of ChIP-Seq (MACS) and Improved peak-calling with MACS2	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
Mash	2.0	mash.readthedocs.io	Mash: fast genome and metagenome distance estimation using MinHash and Mash Screen: high-throughput sequence containment estimation for genome discovery	comparative genomics	`mash`	We don't use this as standalone software, but it is needed by Sourmash, which we use a lot
MEGAHIT	1.2.9	github.com	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	assemblymetagenomics	`megahit`	If you want to assemble genomes from metagenomic data
MetaPhlAn3	3.0	huttenhower.sph.harvard.edu	Metagenomic microbial community profiling using unique clade-specific marker genes	metagenomics	`metaphlan`
MosDepth	0.3.1	github.com	Mosdepth: quick coverage calculation for genomes and exomes	NGS tools	`mosdepth` and `plot-dist.py` for plotting
Mothur	1.44.1	mothur.org	Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities	16S	`mothur`
MultiQC	1.13	multiqc.info	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
Nextflow	20.01.0.5264	www.nextflow.io	unpublished	workflow management	`nextflow`	If you want to set up an automated workflow on our server
Picard tools		broadinstitute.github.io	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
Plink	1.9	www.cog-genomics.org	Second-generation PLINK: rising to the challenge of larger and richer datasets	comparative genomics	`plink`	Used for GWAS and other popgen analyses
Porechop	0.2.4 (no longer maintained/supported)	github.com	unpublished	QA/QC	`porechop`	When you have Nanopore reads and you want to trim off the adapter sequence
Prokka	1.14.6	github.com	Prokka: rapid prokaryotic genome annotation	annotation	`conda activate prokka` then `prokka`	Great for quickly (and accurately) annotating a bacterial genome
QIIME2		qiime2.org	Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2	16S	`source activate qiime2`	Anytime you want to figure out microbial community composition from 16S data
QUAST				QA/QC	quast.py
ROP					/usr/local/bin/rop/rop.sh
RSEM	1.3.0	github.com	RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome	read alignmenttranscriptomics	`rsem-prepare-reference`, `rsem-calculate-expression`, `rsem-tbam2gbam`, `rsem-bam2wig`
samtools	1.7	samtools.sourceforge.net	The Sequence Alignment/Map format and SAMtools	NGS tools	`samtools`	A powerful suite of tools for working with aligment files (bam, sam, etc)
seqtk	1.2-r101-dirty	github.com		working with fasta/fastq	`seqtk`	I use this anytime I want to quickly subsample a fastq file
Sourmash	4.5	sourmash.readthedocs.io	sourmash: a library for MinHash sketching of DNA	metagenomics	`conda activate sourmash` then `sourmash`
seqKit	0.12.0	bioinf.shenwei.me	SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation	working with fasta/fastq	`seqkit`	Anytime you need to manipulate a fastq/a file. Some overlap in functionality with seqtk
Sickle	1.33	github.com	unpublished	QA/QC	`sickle se` or `sickle pe`
snpEff	5.1d	pcingola.github.io	unpublished	SNPs/INDELs	`java -jar /usr/local/bin/snpEff/snpEff.jar` for snpEff and `java -jar /usr/local/bin/snpEff/SnpSift.jar` for snpSift
Sourmash	4.5.0	sourmash.readthedocs.io	Large-scale sequence comparisons with sourmash; and sourmash: a library for MinHash sketching of DNA	comparative genomics	`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.	refseq and genbank microbial reference 'sketches' are in /data/reference_db/sourmash_refs
SPAdes	3.12.0	cab.spbu.ru	SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing	assemblymetagenomics	`spades.py` [options] -o <output_dir>	If you have a metagenomic sequencing data and want to assemble microbial genomes de novo
SQUID	1.4	github.com	SQUID: transcriptomic structural variation detection from RNA-seq	transcriptomics	`squid`	If you have some RNAseq data and want to find fusion and non-fusion transcript sequence variants
SRA toolkit	2.9.1	github.com		public data	`fasterq_dump`, `sam-dump`, and more
STAR	2.6.1c	github.com	STAR: Ultrafast Universal RNA-seq Aligner	read alignment	`STAR` (all caps)	Very fast and popular base-wise aligner	prebuilt STAR indexes for several species present in /data/reference_db/star
Sunbeam		sunbeam.readthedocs.io	Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments	metagenomics	`source activate sunbeam`
Trimmomatic	0.39	www.usadellab.org	Trimmomatic: a flexible trimmer for Illumina sequence data	QA/QC	`java -jar /usr/local/bin/Trimmomatic-0.39/trimmomatic-0.39.jar`	Anytime you need to trim or filter raw reads from a fastq file based on base quality scores or length
Unicycler	0.4.8	github.com	Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads	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	0.1.16	github.com		variants	`vcftools`