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Yu Sugihara (TSL) committed Mar 18, 2022
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Bulked segregant analysis, as implemented in MutMap ([Abe et al., 2012](https://www.nature.com/articles/nbt.2095)), is a powerful and efficient method to identify agronomically important loci in crop plants. MutMap requires whole-genome resequencing of a single individual from the original cultivar and the pooled sequences of F2 progeny from a cross between the original cultivar and mutant. MutMap uses the sequence of the original cultivar to polarize the site frequencies of neighbouring markers and identifies loci with an unexpected site frequency, simulating the genotype of F2 progeny. **The updated pipeline is approximately 5-8 times faster than the previous pipeline, are easier for novice users to use and can be easily installed through bioconda with all dependencies.**

#### Citation
- Akira Abe, Shunichi Kosugi, Kentaro Yoshida, Satoshi Natsume, Hiroki Takagi, Hiroyuki Kanzaki, Hideo Matsumura, Kakoto Yoshida, Chikako Mitsuoka, Muluneh Tamiru, Hideki Innan, Liliana Cano, Sophien Kamoun & Ryohei Terauchi (2012). Genome sequencing reveals agronomically important loci in rice using MutMap. Nature Biotechnol. 30:174-179. [[URL]](https://www.nature.com/articles/nbt.2095)
- Yu Sugihara, Lester Young, Hiroki Yaegashi, Satoshi Natsume, Daniel J. Shea, Hiroki Takagi, Helen Booker, Hideki Innan, Ryohei Terauchi, Akira Abe (2020). High performance pipeline for MutMap and QTL-seq.[[URL]](https://www.biorxiv.org/content/10.1101/2020.06.28.176586v1.full.pdf)
- :zap:**NEW**:zap: Yu Sugihara, Lester Young, Hiroki Yaegashi, Satoshi Natsume, Daniel J. Shea, Hiroki Takagi, Helen Booker, Hideki Innan, Ryohei Terauchi, Akira Abe (2022). [High performance pipeline for MutMap and QTL-seq](https://doi.org/10.7717/peerj.13170). PeerJ, 10:e13170.

- Akira Abe, Shunichi Kosugi, Kentaro Yoshida, Satoshi Natsume, Hiroki Takagi, Hiroyuki Kanzaki, Hideo Matsumura, Kakoto Yoshida, Chikako Mitsuoka, Muluneh Tamiru, Hideki Innan, Liliana Cano, Sophien Kamoun & Ryohei Terauchi (2012). [Genome sequencing reveals agronomically important loci in rice using MutMap](https://www.nature.com/articles/nbt.2095). Nature Biotechnol. 30:174-179.

## Installation
### Dependencies
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