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Sequence Analysis
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.
ClustalW: Multiple Sequence Alignment.
Samtools: Used for manipulating NGS data
BWA: Used for mapping NGS reads against large reference genome
BWA-MEM2: Used for mapping NGS reads against large reference genome (Faster than BWA)
wgsim: Simulate sequence reads from a reference genome
ART: Next-generation sequencing read simulator
Sambamba: Processing of NGS alignment formats
fastp: Preprocessing for FastQ file.
seqtk: Processing sequences in the FASTA or FASTQ format
BBMap: Short read aligner for DNA and RNA-seq data
Roary: Calculates the pan genome and core genome.
Scoary: Pan-genome wide association studies (Pan-GWAS).
SnpEff: Genomic variant annotations and functional effect prediction
Snippy: Finds SNPs between a haploid reference genome and sequence isolates.
snipit: summarise snps relative to your reference sequence.
Prokka: Rapid prokaryotic genome annotation.
CRISPRCasFinder: Detect CRISPR repeats and cas genes from the bacterial genomic sequence
RNAmmer: Predict and annotate ribosomal RNA
Ribodetector: Detect and remove rRNA sequences from metagenomeic, metatranscriptomic, and ncRNA sequencing data
FIMO: Searches a set of sequences for occurrences of known motifs.
OrthoVenn: Comparison and annotation of orthologous gene clusters.
Easyfig: Make genome comparison figure
QUAST: Genome assembly evaluation tool
ClonalFrameML: Inference of recombination in bacterial genomes.
Gubbins: Recombination predictions in bacterial genomes.
Mykrobe: Prediction of Antimicrobial resistance and Lineage in Mycobacterium tuberculosis.
RD-Analyzer: In silico region of difference (RD) analysis of Mycobacterium tuberculosis complex.
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.
Kipoi: Model zoo for genomics