Platanus

BactSNP

BactSNP is a tool to identify SNPs among bacterial isolates. BactSNP can detect SNPs and create a simple TSV file with SNP information as well as an alignment FASTA file containing reconstructed pseudo-genomes of the target isolates in a one-step process.

Program Downloads

BactSNP program can be downloaded from GitHub. Please visit the GitHub site.

Test data Downloads

We prepare a test suite for BactSNP. Users and developers can download the data, and check whether BactSNP works properly by the following commands:

tar xf test.tgz
cd test
./test.sh

Benchmark data Downloads

Simulated reads and the correct SNPs used for the benchmarks described in our paper “Evaluation of SNP calling methods for closely related bacterial isolates and a novel high-accuracy pipeline: BactSNP” is available at the following links.

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case1 case2 case3 case4 case5 case6 case7 case8 case9 case10

case1 case2 case3 case4 case5 case6 case7 case8 case9 case10

case1 case2 case3 case4 case5 case6 case7 case8 case9 case10

case1 case2 case3 case4 case5 case6 case7 case8 case9 case10