Home
Software
Brucellosis Incidence
Brucella Prevalence
Software Tutorial
Prokka
Prokaryotic genome annotation
snippy
Snippy finds SNPs between a haploid reference genome and your NGS sequence reads
ABRicate
Mass screening of contigs for antimicrobial and virulence genes
FASTTREE
build maximum-likelihood phylogenetic trees
Shovill
Assemble bacterial isolate genomes from Illumina paired-end reads
Snippy
Use Test Data and Preset Parameters
Single-end reads, Paired-end reads, Contigs
Single
Paired
Contigs
Upload single-end fastaq reads (--se)
Upload single-end fastaq reads. (Required)
upload
Upload paired-end fastaq reads. (--peil)
Upload paired-end fastaq reads. (Required)
upload
Upload fasta contigs. (--ctgs)
Upload fasta contigs. (Required)
upload
Using a fasta/embl/genbank file as the reference sequence (--reference)
Upload a fasta/embl/genbank file. (Required)
upload
Minimum mapping quality
Minimum mapping quality to allow
60
Minimum coverage
Minimum coverage to call a snp
10
Citation(s)
Seemann T.
Snippy: fast bacterial variant calling from NGS reads.
https://github.com/tseemann/snippy