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tigmint.bib
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@article{Chin_2016, title={Phased diploid genome assembly with single-molecule real-time sequencing}, volume={13}, ISSN={1548-7105}, url={https://doi.org/10.1038/nmeth.4035}, DOI={10.1038/nmeth.4035}, number={12}, journal={Nature Methods}, publisher={Springer Nature}, author={Chin, Chen-Shan and Peluso, Paul and Sedlazeck, Fritz J and Nattestad, Maria and Concepcion, Gregory T and Clum, Alicia and Dunn, Christopher and O’Malley, Ronan and Figueroa-Balderas, Rosa and Morales-Cruz, Abraham and et al.}, year={2016}, month={Oct}, pages={1050–1054}}
@article{Elyanow_2017, title={Identifying structural variants using linked-read sequencing data}, url={https://doi.org/10.1101/190454}, DOI={10.1101/190454}, publisher={Cold Spring Harbor Laboratory}, author={Elyanow, Rebecca and Wu, Hsin-Ta and Raphael, Benjamin J}, year={2017}, month={Sep}}
@article{Gr_ning_2018, title={Bioconda: sustainable and comprehensive software distribution for the life sciences}, volume={15}, ISSN={1548-7105}, url={https://doi.org/10.1038/s41592-018-0046-7}, DOI={10.1038/s41592-018-0046-7}, number={7}, journal={Nature Methods}, publisher={Springer Nature}, author={Grüning, Björn and Dale, Ryan and Sjödin, Andreas and Chapman, Brad A. and Rowe, Jillian and Tomkins-Tinch, Christopher H. and Valieris, Renan and Köster, Johannes}, year={2018}, month={Jul}, pages={475–476}}
@article{Gurevich_2013, title={QUAST: quality assessment tool for genome assemblies}, volume={29}, ISSN={1367-4803}, url={https://doi.org/10.1093/bioinformatics/btt086}, DOI={10.1093/bioinformatics/btt086}, number={8}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Gurevich, Alexey and Saveliev, Vladislav and Vyahhi, Nikolay and Tesler, Glenn}, year={2013}, month={Feb}, pages={1072–1075}}
@article{Jackman_2016, title={{Linuxbrew and Homebrew for cross-platform package management [v1; not peer reviewed]}}, volume={5(ISCB Comm J)}, url={https://doi.org/10.7490/f1000research.1112681.1}, DOI={10.7490/f1000research.1112681.1}, journal={F1000Research}, publisher={F1000 Research, Ltd.}, author={Jackman, Shaun D and Birol, Inanc}, year={2016}, month={Jul}, pages={1795 (poster)}}
@article{Jackman_2017, title={ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter}, volume={27}, ISSN={1549-5469}, url={https://doi.org/10.1101/gr.214346.116}, DOI={10.1101/gr.214346.116}, number={5}, journal={Genome Research}, publisher={Cold Spring Harbor Laboratory}, author={Jackman, Shaun D. and Vandervalk, Benjamin P. and Mohamadi, Hamid and Chu, Justin and Yeo, Sarah and Hammond, S. Austin and Jahesh, Golnaz and Khan, Hamza and Coombe, Lauren and Warren, Rene L. and et al.}, year={2017}, month={Feb}, pages={768–777}}
@article{Jain_2018, title={Nanopore sequencing and assembly of a human genome with ultra-long reads}, volume={36}, ISSN={1546-1696}, url={https://doi.org/10.1038/nbt.4060}, DOI={10.1038/nbt.4060}, number={4}, journal={Nature Biotechnology}, publisher={Springer Nature}, author={Jain, Miten and Koren, Sergey and Miga, Karen H and Quick, Josh and Rand, Arthur C and Sasani, Thomas A and Tyson, John R and Beggs, Andrew D and Dilthey, Alexander T and Fiddes, Ian T and et al.}, year={2018}, month={Jan}, pages={338–345}}
@article{Jiao_2017, title={Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data}, volume={27}, ISSN={1549-5469}, url={https://doi.org/10.1101/gr.213652.116}, DOI={10.1101/gr.213652.116}, number={5}, journal={Genome Research}, publisher={Cold Spring Harbor Laboratory}, author={Jiao, Wen-Biao and Accinelli, Gonzalo Garcia and Hartwig, Benjamin and Kiefer, Christiane and Baker, David and Severing, Edouard and Willing, Eva-Maria and Piednoel, Mathieu and Woetzel, Stefan and Madrid-Herrero, Eva and et al.}, year={2017}, month={Feb}, pages={778–786}}
@article{Krzywinski_2009, title={Circos: An information aesthetic for comparative genomics}, volume={19}, ISSN={1088-9051}, url={https://doi.org/10.1101/gr.092759.109}, DOI={10.1101/gr.092759.109}, number={9}, journal={Genome Research}, publisher={Cold Spring Harbor Laboratory}, author={Krzywinski, M. and Schein, J. and Birol, I. and Connors, J. and Gascoyne, R. and Horsman, D. and Jones, S. J. and Marra, M. A.}, year={2009}, month={Jun}, pages={1639–1645}}
@article{Kuleshov_2016, title={Genome assembly from synthetic long read clouds}, volume={32}, ISSN={1460-2059}, url={https://doi.org/10.1093/bioinformatics/btw267}, DOI={10.1093/bioinformatics/btw267}, number={12}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Kuleshov, Volodymyr and Snyder, Michael P. and Batzoglou, Serafim}, year={2016}, month={Jun}, pages={i216–i224}}
@article{Li_2009, title={The Sequence Alignment/Map format and SAMtools}, volume={25}, ISSN={1460-2059}, url={https://doi.org/10.1093/bioinformatics/btp352}, DOI={10.1093/bioinformatics/btp352}, number={16}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Li, H. and Handsaker, B. and Wysoker, A. and Fennell, T. and Ruan, J. and Homer, N. and Marth, G. and Abecasis, G. and Durbin, R.}, year={2009}, month={Jun}, pages={2078–2079}}
@article{Li_2013, title={{Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM}}, author={Li, Heng}, journal={arXiv:1303.3997}, year={2013}}
@article{Li_2017, title={Minimap2: versatile pairwise alignment for nucleotide sequences}, journal={arXiv:1708.01492}, author={Li, Heng}, year={2017}}
@article{Luo_2017, title={LRSim: a Linked Reads Simulator generating insights for better genome partitioning}, url={https://doi.org/10.1101/103549}, DOI={10.1101/103549}, publisher={Cold Spring Harbor Laboratory}, author={Luo, Ruibang and Sedlazeck, Fritz J and Darby, Charlotte A and Kelly, Stephen M and Schatz, Michael C}, year={2017}, month={Jan}}
@article{Mostovoy_2016, title={A hybrid approach for de novo human genome sequence assembly and phasing}, volume={13}, ISSN={1548-7105}, url={https://doi.org/10.1038/nmeth.3865}, DOI={10.1038/nmeth.3865}, number={7}, journal={Nature Methods}, publisher={Springer Nature}, author={Mostovoy, Yulia and Levy-Sakin, Michal and Lam, Jessica and Lam, Ernest T and Hastie, Alex R and Marks, Patrick and Lee, Joyce and Chu, Catherine and Lin, Chin and Džakula, Željko and et al.}, year={2016}, month={May}, pages={587–590}}
@article{Murphy_2015, title={NxRepair: error correction inde novosequence assembly using Nextera mate pairs}, volume={3}, ISSN={2167-8359}, url={https://doi.org/10.7717/peerj.996}, DOI={10.7717/peerj.996}, journal={PeerJ}, publisher={PeerJ}, author={Murphy, Rebecca R. and O’Connell, Jared and Cox, Anthony J. and Schulz-Trieglaff, Ole}, year={2015}, month={Jun}, pages={e996}}
@article{O_Connell_2014, title={NxTrim: optimized trimming of Illumina mate pair reads}, url={https://doi.org/10.1101/007666}, DOI={10.1101/007666}, publisher={Cold Spring Harbor Laboratory}, author={O’Connell, Jared and Schulz-Trieglaff, Ole and Carlson, Emma and Hims, Matthew M and Gormley, Niall A and Cox, Anthony J}, year={2014}, month={Aug}}
@article{Quinlan_2010, title={BEDTools: a flexible suite of utilities for comparing genomic features}, volume={26}, ISSN={1367-4803}, url={https://doi.org/10.1093/bioinformatics/btq033}, DOI={10.1093/bioinformatics/btq033}, number={6}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Quinlan, Aaron R. and Hall, Ira M.}, year={2010}, month={Jan}, pages={841–842}}
@article{Sahlin_2016, title={Assembly scaffolding with PE-contaminated mate-pair libraries}, volume={32}, ISSN={1460-2059}, url={https://doi.org/10.1093/bioinformatics/btw064}, DOI={10.1093/bioinformatics/btw064}, number={13}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Sahlin, Kristoffer and Chikhi, Rayan and Arvestad, Lars}, year={2016}, month={Mar}, pages={1925–1932}}
@article{Spies_2017, title={Genome-wide reconstruction of complex structural variants using read clouds}, volume={14}, ISSN={1548-7105}, url={https://doi.org/10.1038/nmeth.4366}, DOI={10.1038/nmeth.4366}, number={9}, journal={Nature Methods}, publisher={Springer Nature}, author={Spies, Noah and Weng, Ziming and Bishara, Alex and McDaniel, Jennifer and Catoe, David and Zook, Justin M and Salit, Marc and West, Robert B and Batzoglou, Serafim and Sidow, Arend}, year={2017}, month={Jul}, pages={915–920}}
@article{Sudmant_2015, title={An integrated map of structural variation in 2,504 human genomes}, volume={526}, ISSN={1476-4687}, url={https://doi.org/10.1038/nature15394}, DOI={10.1038/nature15394}, number={7571}, journal={Nature}, publisher={Springer Nature}, author={Sudmant, Peter H. and Rausch, Tobias and Gardner, Eugene J. and Handsaker, Robert E. and Abyzov, Alexej and Huddleston, John and Zhang, Yan and Ye, Kai and Jun, Goo and et al.}, year={2015}, month={Oct}, pages={75–81}}
@article{Walker_2014, title={Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement}, volume={9}, ISSN={1932-6203}, url={https://doi.org/10.1371/journal.pone.0112963}, DOI={10.1371/journal.pone.0112963}, number={11}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Walker, Bruce J. and Abeel, Thomas and Shea, Terrance and Priest, Margaret and Abouelliel, Amr and Sakthikumar, Sharadha and Cuomo, Christina A. and Zeng, Qiandong and Wortman, Jennifer and Young, Sarah K. and et al.}, editor={Wang, JunwenEditor}, year={2014}, month={Nov}, pages={e112963}}
@article{Warren_2015, title={LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads}, volume={4}, ISSN={2047-217X}, url={https://doi.org/10.1186/s13742-015-0076-3}, DOI={10.1186/s13742-015-0076-3}, number={1}, journal={GigaScience}, publisher={Oxford University Press (OUP)}, author={Warren, René L. and Yang, Chen and Vandervalk, Benjamin P. and Behsaz, Bahar and Lagman, Albert and Jones, Steven J. M. and Birol, Inanç}, year={2015}, month={Aug}}
@article{Weisenfeld_2017, title={Direct determination of diploid genome sequences}, volume={27}, ISSN={1549-5469}, url={https://doi.org/10.1101/gr.214874.116}, DOI={10.1101/gr.214874.116}, number={5}, journal={Genome Research}, publisher={Cold Spring Harbor Laboratory}, author={Weisenfeld, Neil I. and Kumar, Vijay and Shah, Preyas and Church, Deanna M. and Jaffe, David B.}, year={2017}, month={Apr}, pages={757–767}}
@article{Yeo_2017, title={ARCS: scaffolding genome drafts with linked reads}, volume={34}, ISSN={1460-2059}, url={https://doi.org/10.1093/bioinformatics/btx675}, DOI={10.1093/bioinformatics/btx675}, number={5}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Yeo, Sarah and Coombe, Lauren and Warren, René L and Chu, Justin and Birol, Inanç}, editor={Sahinalp, CenkEditor}, year={2017}, month={Oct}, pages={725–731}}
@article{Zheng_2016, title={Haplotyping germline and cancer genomes with high-throughput linked-read sequencing}, volume={34}, ISSN={1546-1696}, url={https://doi.org/10.1038/nbt.3432}, DOI={10.1038/nbt.3432}, number={3}, journal={Nature Biotechnology}, publisher={Springer Nature}, author={Zheng, Grace X Y and Lau, Billy T and Schnall-Levin, Michael and Jarosz, Mirna and Bell, John M and Hindson, Christopher M and Kyriazopoulou-Panagiotopoulou, Sofia and Masquelier, Donald A and Merrill, Landon and Terry, Jessica M and et al.}, year={2016}, month={Feb}, pages={303–311}}
@article{Zook_2016, title={Extensive sequencing of seven human genomes to characterize benchmark reference materials}, volume={3}, ISSN={2052-4463}, url={https://doi.org/10.1038/sdata.2016.25}, DOI={10.1038/sdata.2016.25}, journal={Scientific Data}, publisher={Springer Nature}, author={Zook, Justin M. and Catoe, David and McDaniel, Jennifer and Vang, Lindsay and Spies, Noah and Sidow, Arend and Weng, Ziming and Liu, Yuling and Mason, Christopher E. and Alexander, Noah and et al.}, year={2016}, month={Jun}, pages={160025}}
@online{URL_10x, title={{Overview of Genome Software}}, author={{10x Genomics}}, url={https://support.10xgenomics.com/genome-exome/software/overview/welcome}, urldate={2018-06-01}}
@online{URL_Topsorter, title={Topsorter: Graphical assessment of structrial variants using 10x genomics data}, author={Han Fang}, url={https://github.com/hanfang/Topsorter}, urldate={2018-06-01}}
@online{URL_JupiterPlot, title={JupiterPlot: Circos Assembly Consistency plot}, author={Justin Chu}, url={https://github.com/JustinChu/JupiterPlot}, urldate={2018-06-01}}