Tools

Search, containers, workflows

• Search for tools: https://bio.tools/
• BioContainers: containers for bioinformatics: https://biocontainers.pro/#/
• Docker Hub: docker containers: https://hub.docker.com/
• nf-core: Nextflow workflows: https://nf-co.re/

Commonly-used tools

BLAST Sequence matching: https://blast.ncbi.nlm.nih.gov/Blast.cgi

• Paper: A Guide to BLAST: https://f1000research.com/documents/7-1435
• Tutorial: BLAST: https://isugenomics.github.io/bioinformatics-workbook/dataAnalysis/blast/blast_index

bwa Map sequences against reference database: https://github.com/lh3/bwa

minimap2 Map long read sequences against reference database: https://github.com/lh3/minimap2

Samtools Tools for processing alignment files: https://www.htslib.org/

Spades Genome assembly: http://cab.spbu.ru/software/spades/

Freebayes Variant calling: https://github.com/ekg/freebayes

IQ-Tree Phylogenetics: http://www.iqtree.org/

Mothur Metagenomics: https://www.mothur.org/