Sequence Analysis

Sequence Alignment

ViralMSA: Reference-guided multiple sequence alignment of viral genomes.

Aliview: Alignment viewer and editor

MAFFT: Tool to create multiple sequence alignment based on progressive alignment algorithm.

Mauve: Tool to create multiple sequence alignment based on progressive alignment and alignment display.

NGS analysis

fastp: Preprocessing for FastQ file.

seqtk: Processing sequences in the FASTA or FASTQ format

BBMap: Short read aligner for DNA and RNA-seq data

Pan Genome Pipeline

Roary: Calculates the pan genome and core genome.

Genome-wide association study (GWAS)

Scoary: Pan-genome wide association studies (Pan-GWAS).

SNP Analysis

Snippy: Finds SNPs between a haploid reference genome and sequence isolates.

snipit: summarise snps relative to your reference sequence.

Genome Annotation

Prokka: Rapid prokaryotic genome annotation.

Motif Finder

FIMO: Searches a set of sequences for occurrences of known motifs.

Comparative genomics

OrthoVenn: Comparison and annotation of orthologous gene clusters.

Easyfig: Make genome comparison figure

Recombination

ClonalFrameML: Inference of recombination in bacterial genomes.

Gubbins: Recombination predictions in bacterial genomes.

Antimicrobial resistance and lineage prediction

Mykrobe: Prediction of Antimicrobial resistance and Lineage in Mycobacterium tuberculosis.

RD-Analyzer: In silico region of difference (RD) analysis of Mycobacterium tuberculosis complex.

Mobile Genetic Elements (MGEs) Analysis

MobileElementFinder: Identify Mobile Genetic Elements (MGEs) in Bacterial Genome

PHAST (PHAge Search Tool): Identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids (Online).

ISEScan: Identify IS (Insertion Sequence) elements in genome.