georgiesamaha / BioinformaticsResources

List of tools and quick commands for various bioinformatics methods and datasets

BioinformaticsResources

List of tools for various bioinformatics methods and datasets

NGS data processing

Genomics

Data type	Tool	Function	Input requirements	Resources
WGS	Slivar	Population-based annotation, filter variants	vcf.gz	Wiki
WGS	SURVIVOR	Filter, merge, evaluate structural variants	vcf (not .gz)	Wiki
WGS	BCFtools	Filter, merge, subset, evaluate vcfs	vcf.gz	Cheatsheet
WGS	Hap.py	Gold standard vcf comparison tool (haplotype based)	vcf.gz	Bio validation
WGS	GRIDSS2	Structural variant caller	bam	Wiki
Array, WGS	Plink	Everything	vcf, bcf, plink
Array	SNPflip	find reverse and ambiguous strand SNPs	plink .bim
Reference	Liftoff	remap annotations between assemblies	gff, gtf
WGS	VCFvalidator	Validate vcf integrity	vcf.gz vcf.bz2
WGS	LINX	Somatic structural variant classification	vcf	Visualisation
WGS	PURPLE	Tumour purity and ploidy estimator	bam, vcf	GPL pipeline

RNAseq

Data type	Tool	Function	Input requirements	Resources
RNAseq	TMPcalculator	find reverse and ambiguous strand SNPs	bam, gtf
RNAseq	DESeq2	differential expression	count matrix
RNAseq	RNA-seqlopedia	gene expression, annotation,splicing
scRNAseq	Single cell RNAseq course

De novo transcriptomics

Data type	Tool	Function	Input requirements	Resources
De novo transcriptomics	Trinity runtime profiling	Understand resource requirements of a trinity run	NA
De novo transcriptomics	Trinity benchmarking	Understand resource requirements of a trinity run	NA

Pipeline/workflow management

Nextflow

DIY Nextflow tutorial
Building DSL2 pipelines

Galaxy

Galaxy training network

Useful curated bioinformatics script and resource repos

Who	Repo	Utility
PeterMac	PMCC	plotting, fastqc, rnaseq, performance, filtering
AstrobioMike	Bioinformatics Tools	filtering, db querying
davfre	SAM and BAM oneliners	read counting, filtering
EBI	EBI Variation	various
Hartwig medical foundation	HMFtools	Various WGS
Daniel Cook	Awesome bioinformatics	curated resource lists
nf-core	nf-core tools	nf-core helper scripts
AWS	amazon-genomics-cli	tool to simplify the processes of deploying the AWS infrastructure
BioWulf	GATK benchmarking	benchmarking, scalability of GATK commands
Xiaole Shirley Liu et al.	Introduction to Bioinformatics and Computational Biology	Course material for STAT115/215 BIO/BST282 at Harvard University

Compute resource profiling

Tool	Platform
async-profiler	cloud, VM
HPC usage reports	HPC, Artemis, Gadi, Flashlite
Memray	cloud, VM
NetData	VM, cloud

Plotting

vcfR
CMplot
ggsashimi
BioCircos
karyotypeR
samplot
colourfindr
NanoPlot
Raincloud plots
chromoMap
nVennR
HaplotypePlot
Ideogram
R graph grammar
DiscoPlot