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SF_Snippy Shovill Prokka ABRicate FastTree

Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (SNPs) and insertions/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is designed with speed in mind, and produces a consistent set of output files in a single folder. It can then take a set of Snippy results using the same reference and generate a core SNP alignment.

Snippy

To call SNPs between haploid references and interested NGS reads
Use Test Data and Preset Parameters
Single-end reads, Paired-end reads, Contigs
Upload fasta contigs. (--ctgs)
Upload fasta contigs. (Required)
Using a fasta/embl/genbank file as the reference sequence (--reference)
Upload a fasta/embl/genbank file. (Required)
Minimum mapping quality
Minimum mapping quality to allow
Minimum coverage
Minimum coverage to call a snp

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