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.
- S.aureus
- 99.9% identity cases TreeToReads
case1 case2 case3 case4 case5 case6 case7 case8 case9 case10
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- 99% identity cases TreeToReads
case1 case2 case3 case4 case5 case6 case7 case8 case9 case10
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- 98% identity cases TreeToReads
case1 case2 case3 case4 case5 case6 case7 case8 case9 case10
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- 97% identity cases TreeToReads
case1 case2 case3 case4 case5 case6 case7 case8 case9 case10
- N. meningitidis
- 99.9% identity cases TreeToReads
case1 case2 case3 case4 case5 case6 case7 case8 case9 case10
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- 99% identity cases TreeToReads
case1 case2 case3 case4 case5 case6 case7 case8 case9 case10
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- 98% identity cases TreeToReads
case1 case2 case3 case4 case5 case6 case7 case8 case9 case10
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- 97% identity cases TreeToReads
case1 case2 case3 case4 case5 case6 case7 case8 case9 case10
- E.coli
- 99.9% identity cases TreeToReads
case1 case2 case3 case4 case5 case6 case7 case8 case9 case10
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- 99% identity cases TreeToReads
case1 case2 case3 case4 case5 case6 case7 case8 case9 case10
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- 98% identity cases TreeToReads
case1 case2 case3 case4 case5 case6 case7 case8 case9 case10
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- 97% identity cases TreeToReads
case1 case2 case3 case4 case5 case6 case7 case8 case9 case10