tools
An overview of all bioinformatics tools and pipelines developed and described in this blog.
| Tool | Description | Blog post |
|---|---|---|
phage_assembly_snakemake | Snakemake pipeline for bacteriophage genome assembly from Illumina paired-end reads using Shovill; includes fastp QC, QUAST, VirSorter2, CheckV, and automated HTML/PDF reports. | Two New Snakemake Pipelines for Bacteriophage Assembly and QC: Illumina and Nanopore |
phage-nanopore-assembly-snakemake | Snakemake pipeline for bacteriophage genome assembly from Oxford Nanopore reads using Flye with Medaka polishing; includes NanoPlot QC, Filtlong, Porechop_ABI, Bandage, VirSorter2, CheckV, and automated HTML/PDF reports. | Two New Snakemake Pipelines for Bacteriophage Assembly and QC: Illumina and Nanopore |
rssc_sequevar_typing | Snakemake pipeline for automated RSSC sequevar typing: extracts the egl gene via in-silico PCR, aligns against 58 curated reference sequevars with MAFFT, builds a maximum-likelihood phylogenetic tree with IQ-TREE2, and assigns phylotype and sequevar per genome. | Rapid and Reproducible RSSC Sequevar Typing with Snakemake |
nanopore_autocycler_snakemake | Snakemake pipeline for high-quality bacterial genome assembly from Oxford Nanopore reads using Autocycler consensus (Canu, Flye, Plassembler); includes read QC, Racon/Medaka polishing, BUSCO/CheckM2/QUAST assessment, and automated HTML/PDF reports. | Superior Bacterial Genome Assembly with Autocycler Consensus and Snakemake |
illumina-bacterial-assembly-snakemake | Snakemake pipeline for bacterial genome assembly from Illumina paired-end reads with QC (QUAST, CheckM2, BUSCO, Kraken2, GTDB-Tk) and automated HTML/PDF reports. | Adventures in Bacterial Genome Assembly with Snakemake |
bacterial-assembly-qc-snakemake | QC-only Snakemake pipeline for existing bacterial assemblies; runs QUAST, CheckM2, BUSCO, generates summary plots and Excel reports without re-assembling. | Adventures in Bacterial Genome Assembly with Snakemake |
nanopore_only_snakemake | Snakemake pipeline for bacterial genome assembly and QC from Oxford Nanopore long reads. | Adventures in Bacterial Genome Assembly with Snakemake |
qpcr-primer-analyzer-ilvo | Single-file web tool for evaluating primer/probe sets for qPCR assays. Calculates salt-corrected melting temperatures, detects hairpins and cross-dimers, and checks compatibility with Thermo Fisher guidelines. | Introducing the qPCR Primer Analyzer ILVO |
run_epcr.py | Python script for batch in-silico PCR and probe finding across folders of genome FASTA files. Supports IUPAC ambiguity codes, fuzzy matching, multi-threading, and outputs TSV tables, FASTA amplicons, and amplicon count matrices. | Batch In-Silico (q)PCR Made Easy with run_epcr.py |