GFF Utilities: GffRead and GffCompare [version 2; peer review: 3 approved] von Pertea, Geo, Pertea, Mihaela

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GFF Utilities: GffRead and GffCompare von Pertea, Geo, Pertea, Mihaela

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Improved transcriptome assembly using a hybrid of long and short reads with StringTie von Shumate, Alaina, Wong, Brandon, Pertea, Geo, Pertea, Mihaela

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Transcriptome assembly from long-read RNA-seq alignments with StringTie2 von Kovaka, Sam, Zimin, Aleksey V, Pertea, Geo M, Razaghi, Roham, Salzberg, Steven L, Pertea, Mihaela

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The human transcriptome: an unfinished story von Pertea, Mihaela

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BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis von Bouckaert, Remco, Vaughan, Timothy G, Barido-Sottani, Joëlle, Duchêne, Sebastián, Fourment, Mathieu, Gavryushkina, Alexandra, Heled, Joseph, Jones, Graham, Kühnert, Denise, De Maio, Nicola, Matschiner, Michael, Mendes, Fábio K, Müller, Nicola F, Ogilvie, Huw A, du Plessis, Louis, Popinga, Alex, Rambaut, Andrew, Rasmussen, David, Siveroni, Igor, Suchard, Marc A, Wu, Chieh-Hsi, Xie, Dong, Zhang, Chi, Stadler, Tanja, Drummond, Alexei J

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RESCRIPt: Reproducible sequence taxonomy reference database management von Robeson, Michael S., O'Rourke, Devon R., Kaehler, Benjamin D., Ziemski, Michal, Dillon, Matthew R., Foster, Jeffrey T., Bokulich, Nicholas A.

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CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise von Pertea, Mihaela, Shumate, Alaina, Pertea, Geo, Varabyou, Ales, Breitwieser, Florian P, Chang, Yu-Chi, Madugundu, Anil K, Pandey, Akhilesh, Salzberg, Steven L

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Tximeta: Reference sequence checksums for provenance identification in RNA-seq von Love, Michael I., Soneson, Charlotte, Hickey, Peter F., Johnson, Lisa K., Pierce, N. Tessa, Shepherd, Lori, Morgan, Martin, Patro, Rob

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Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation von Ramsey, Jolene, Rasche, Helena, Maughmer, Cory, Criscione, Anthony, Mijalis, Eleni, Liu, Mei, Hu, James C., Young, Ry, Gill, Jason J.

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Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks von Wick, Ryan R, Judd, Louise M, Holt, Kathryn E

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ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization von Garrido-Martín, Diego, Palumbo, Emilio, Guigó, Roderic, Breschi, Alessandra

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scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data von Tian, Luyi, Su, Shian, Dong, Xueyi, Amann-Zalcenstein, Daniela, Biben, Christine, Seidi, Azadeh, Hilton, Douglas J, Naik, Shalin H, Ritchie, Matthew E

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PhANNs, a fast and accurate tool and web server to classify phage structural proteins von Cantu, Vito Adrian, Salamon, Peter, Seguritan, Victor, Redfield, Jackson, Salamon, David, Edwards, Robert A., Segall, Anca M.

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PlasClass improves plasmid sequence classification von Pellow, David, Mizrahi, Itzik, Shamir, Ron

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Memes: A motif analysis environment in R using tools from the MEME Suite von Nystrom, Spencer L., McKay, Daniel J.

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Between a chicken and a grape: estimating the number of human genes von Pertea, Mihaela, Salzberg, Steven L

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Splam: a deep-learning-based splice site predictor that improves spliced alignments von Chao, Kuan-Hao, Mao, Alan, Salzberg, Steven L, Pertea, Mihaela

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Effects of transcriptional noise on estimates of gene and transcript expression in RNA sequencing experiments von Varabyou, Ales, Salzberg, Steven L., Pertea, Mihaela

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Major data analysis errors invalidate cancer microbiome findings von Gihawi, Abraham, Ge, Yuchen, Lu, Jennifer, Puiu, Daniela, Xu, Amanda, Cooper, Colin S., Brewer, Daniel S., Pertea, Mihaela, Salzberg, Steven L.

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