From ea6546df48d9348ed6c6ad4eb473db36bda637b2 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Mon, 16 Oct 2023 15:25:37 +1000 Subject: [PATCH 1/7] citations: Improve them. --- docs/citations.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/docs/citations.md b/docs/citations.md index cdd147c9..cdf81089 100755 --- a/docs/citations.md +++ b/docs/citations.md @@ -10,6 +10,9 @@ You should cite all of these tools as well, or whichever tools you know that you we have provided the following list of citations for you to use in alphabetical order. This list will be updated as new modules are added to aviary. +## Aviary +- **Aviary**: Newell. R.J.P., Tyson G.W., Woodcroft B.J. Available at https://github.com/rhysnewell/aviary + ## QC - **NanoPack**: De Coster, W., D’Hert, S., Schultz, D. T., Cruts, M. & Van Broeckhoven, C. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics 34, 2666–2669 (2018). https://doi.org/10.1093/bioinformatics/bty149 - **NanoPack2**: De Coster, W. & Rademakers, R. NanoPack2: population-scale evaluation of long-read sequencing data. Bioinformatics 39, (2023). https://doi.org/10.1093/bioinformatics/btad311 @@ -33,8 +36,7 @@ modules are added to aviary. - **VAMB**: Nissen, J. N. et al. Improved metagenome binning and assembly using deep variational autoencoders. Nature Biotechnology 1–6 (2021) doi:10.1038/s41587-020-00777-4. https://doi.org/10.1038/s41587-020-00777-4 - **MetaBAT**: Kang, D. D., Froula, J., Egan, R. & Wang, Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 3, e1165 (2015). https://doi.org/10.7717/peerj.1165 - **MetaBAT2**: Kang, D. D. et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7, (2019). https://doi.org/10.7717/peerj.7359 -- **DAS Tool**: Sieber, C. M. K. et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nature Microbiology 3, 836–843 (2018). -https://doi.org/10.1038/s41564-018-0171-1 +- **DAS Tool**: Sieber, C. M. K. et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nature Microbiology 3, 836–843 (2018). https://doi.org/10.1038/s41564-018-0171-1 - **SemiBin2**: Pan, S., Zhao, X. M., & Coelho, L. P. (2023). SemiBin2: self-supervised contrastive learning leads to better MAGs for short-and long-read sequencing, Bioinformatics, Volume 39, Issue Supplement_1, June 2023, Pages i21–i29. https://doi.org/10.1093/bioinformatics/btad209 - **MaxBin 2.0**: Wu, Y.-W., Simmons, B. A. & Singer, S. W. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 32, 605–607 (2016). https://doi.org/10.1093/bioinformatics/btv638 - **Rosella**: https://github.com/rhysnewell/rosella @@ -45,6 +47,7 @@ https://doi.org/10.1038/s41564-018-0171-1 - **eggNOG mapper 2**: Cantalapiedra, C. P., Hernández-Plaza, A., Letunic, I., Bork, P., & Huerta-Cepas, J. (2021). eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Molecular biology and evolution, 38(12), 5825-5829. https://doi.org/10.1093/molbev/msab293 - **GTDB-Tk 2**: Chaumeil, P. A., Mussig, A. J., Hugenholtz, P., & Parks, D. H. (2022). GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics, 38(23), 5315-5316. https://doi.org/10.1093/bioinformatics/btac672 - **GraftM**: Boyd, J. A., Woodcroft, B. J. & Tyson, G. W. GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes. Nucleic Acids Research 46, e59 (2018). https://doi.org/10.1093/nar/gky174 +- **CoverM**: Woodcroft B.J., Nissen J., Carmago A., Tyson G.W., Newell. R.J.P., Aroney S. Available at https://github.com/wwood/CoverM ## Variant calling -- **Lorikeet**: https://github.com/rhysnewell/Lorikeet \ No newline at end of file +- **Lorikeet**: McMaster E.S., Craig P., Boden M., Tyson G.W., Woodcroft B.J. Available at https://github.com/rhysnewell/Lorikeet From 296e33b61c845ab73ac07c3bd31ebeeaeca33d31 Mon Sep 17 00:00:00 2001 From: AroneyS Date: Wed, 15 Nov 2023 08:35:14 +1000 Subject: [PATCH 2/7] add Aviary authors from #168 --- docs/citations.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/citations.md b/docs/citations.md index cdf81089..d315794e 100755 --- a/docs/citations.md +++ b/docs/citations.md @@ -11,7 +11,7 @@ we have provided the following list of citations for you to use in alphabetical modules are added to aviary. ## Aviary -- **Aviary**: Newell. R.J.P., Tyson G.W., Woodcroft B.J. Available at https://github.com/rhysnewell/aviary +- **Aviary**: Newell R.J.P., Aroney S.T.N., Zaugg J., Sternes P., Tyson G.W., Woodcroft B.J. Available at https://github.com/rhysnewell/aviary ## QC - **NanoPack**: De Coster, W., D’Hert, S., Schultz, D. T., Cruts, M. & Van Broeckhoven, C. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics 34, 2666–2669 (2018). https://doi.org/10.1093/bioinformatics/bty149 From bc0691c89c7228b53b0ff62993865dae2455b2f0 Mon Sep 17 00:00:00 2001 From: AroneyS Date: Wed, 15 Nov 2023 08:35:50 +1000 Subject: [PATCH 3/7] add Rhys to his own paper --- docs/citations.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/citations.md b/docs/citations.md index d315794e..f6958311 100755 --- a/docs/citations.md +++ b/docs/citations.md @@ -50,4 +50,4 @@ modules are added to aviary. - **CoverM**: Woodcroft B.J., Nissen J., Carmago A., Tyson G.W., Newell. R.J.P., Aroney S. Available at https://github.com/wwood/CoverM ## Variant calling -- **Lorikeet**: McMaster E.S., Craig P., Boden M., Tyson G.W., Woodcroft B.J. Available at https://github.com/rhysnewell/Lorikeet +- **Lorikeet**: Newell R.J.P., McMaster E.S., Craig P., Boden M., Tyson G.W., Woodcroft B.J. Available at https://github.com/rhysnewell/Lorikeet From 7dc9e5cf03df6cc047b354deac4ae718eb4768b7 Mon Sep 17 00:00:00 2001 From: AroneyS Date: Mon, 20 Nov 2023 09:56:53 +1000 Subject: [PATCH 4/7] add CoverM title --- docs/citations.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/citations.md b/docs/citations.md index f6958311..f9dc6bf8 100755 --- a/docs/citations.md +++ b/docs/citations.md @@ -47,7 +47,7 @@ modules are added to aviary. - **eggNOG mapper 2**: Cantalapiedra, C. P., Hernández-Plaza, A., Letunic, I., Bork, P., & Huerta-Cepas, J. (2021). eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Molecular biology and evolution, 38(12), 5825-5829. https://doi.org/10.1093/molbev/msab293 - **GTDB-Tk 2**: Chaumeil, P. A., Mussig, A. J., Hugenholtz, P., & Parks, D. H. (2022). GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics, 38(23), 5315-5316. https://doi.org/10.1093/bioinformatics/btac672 - **GraftM**: Boyd, J. A., Woodcroft, B. J. & Tyson, G. W. GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes. Nucleic Acids Research 46, e59 (2018). https://doi.org/10.1093/nar/gky174 -- **CoverM**: Woodcroft B.J., Nissen J., Carmago A., Tyson G.W., Newell. R.J.P., Aroney S. Available at https://github.com/wwood/CoverM +- **CoverM**: Woodcroft B.J., Nissen J., Carmago A., Tyson G.W., Newell. R.J.P., Aroney S. CoverM: Read mapping statistics for metagenomics. Available at https://github.com/wwood/CoverM ## Variant calling - **Lorikeet**: Newell R.J.P., McMaster E.S., Craig P., Boden M., Tyson G.W., Woodcroft B.J. Available at https://github.com/rhysnewell/Lorikeet From cc44ca9a488b367e30083d53fac3c7f9f91dbf6b Mon Sep 17 00:00:00 2001 From: AroneyS Date: Mon, 20 Nov 2023 10:13:20 +1000 Subject: [PATCH 5/7] update CoverM author order --- docs/citations.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/citations.md b/docs/citations.md index f9dc6bf8..82668da2 100755 --- a/docs/citations.md +++ b/docs/citations.md @@ -47,7 +47,7 @@ modules are added to aviary. - **eggNOG mapper 2**: Cantalapiedra, C. P., Hernández-Plaza, A., Letunic, I., Bork, P., & Huerta-Cepas, J. (2021). eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Molecular biology and evolution, 38(12), 5825-5829. https://doi.org/10.1093/molbev/msab293 - **GTDB-Tk 2**: Chaumeil, P. A., Mussig, A. J., Hugenholtz, P., & Parks, D. H. (2022). GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics, 38(23), 5315-5316. https://doi.org/10.1093/bioinformatics/btac672 - **GraftM**: Boyd, J. A., Woodcroft, B. J. & Tyson, G. W. GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes. Nucleic Acids Research 46, e59 (2018). https://doi.org/10.1093/nar/gky174 -- **CoverM**: Woodcroft B.J., Nissen J., Carmago A., Tyson G.W., Newell. R.J.P., Aroney S. CoverM: Read mapping statistics for metagenomics. Available at https://github.com/wwood/CoverM +- **CoverM**: Woodcroft B.J., Newell. R.J.P., Aroney S. T. N., Nissen J., Carmago A., Tyson G.W. CoverM: Read mapping statistics for metagenomics. Available at https://github.com/wwood/CoverM ## Variant calling - **Lorikeet**: Newell R.J.P., McMaster E.S., Craig P., Boden M., Tyson G.W., Woodcroft B.J. Available at https://github.com/rhysnewell/Lorikeet From d3012dc9a4338a98e7ae92b051a4b81fff018fb1 Mon Sep 17 00:00:00 2001 From: AroneyS Date: Mon, 20 Nov 2023 10:16:17 +1000 Subject: [PATCH 6/7] consistent spacing between initials --- docs/citations.md | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/docs/citations.md b/docs/citations.md index 82668da2..1bd55021 100755 --- a/docs/citations.md +++ b/docs/citations.md @@ -14,17 +14,17 @@ modules are added to aviary. - **Aviary**: Newell R.J.P., Aroney S.T.N., Zaugg J., Sternes P., Tyson G.W., Woodcroft B.J. Available at https://github.com/rhysnewell/aviary ## QC -- **NanoPack**: De Coster, W., D’Hert, S., Schultz, D. T., Cruts, M. & Van Broeckhoven, C. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics 34, 2666–2669 (2018). https://doi.org/10.1093/bioinformatics/bty149 +- **NanoPack**: De Coster, W., D’Hert, S., Schultz, D.T., Cruts, M. & Van Broeckhoven, C. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics 34, 2666–2669 (2018). https://doi.org/10.1093/bioinformatics/bty149 - **NanoPack2**: De Coster, W. & Rademakers, R. NanoPack2: population-scale evaluation of long-read sequencing data. Bioinformatics 39, (2023). https://doi.org/10.1093/bioinformatics/btad311 - **fastp**: Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018). https://doi.org/10.1093/bioinformatics/bty560 ## Assembly -- **Flye**: Kolmogorov, M., Yuan, J., Lin, Y. & Pevzner, P. A. Assembly of long, error-prone reads using repeat graphs. Nature Biotechnology 37, 540–546 (2019). https://doi.org/10.1038/s41587-019-0072-8 +- **Flye**: Kolmogorov, M., Yuan, J., Lin, Y. & Pevzner, P.A. Assembly of long, error-prone reads using repeat graphs. Nature Biotechnology 37, 540–546 (2019). https://doi.org/10.1038/s41587-019-0072-8 - **Medaka**: https://github.com/nanoporetech/medaka - **Racon**: Vaser, R., Sović, I., Nagarajan, N. & Šikić, M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res 27, 737–746 (2017). https://doi.org/10.1101/gr.214270.116 -- **Pilon**: Walker, B. J. et al. Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. PLOS ONE 9, e112963 (2014). https://doi.org/10.1371/journal.pone.0112963 -- **metaSPAdes**: Nurk, S., Meleshko, D., Korobeynikov, A., & Pevzner, P. A. (2017). metaSPAdes: a new versatile metagenomic assembler. Genome research, 27(5), 824-834. https://doi.org/10.1101/gr.213959.116 -- **Unicycler**: Wick, R. R., Judd, L. M., Gorrie, C. L. & Holt, K. E. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLOS Computational Biology 13, e1005595 (2017). https://doi.org/10.1371/journal.pcbi.1005595 +- **Pilon**: Walker, B.J. et al. Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. PLOS ONE 9, e112963 (2014). https://doi.org/10.1371/journal.pone.0112963 +- **metaSPAdes**: Nurk, S., Meleshko, D., Korobeynikov, A., & Pevzner, P.A. (2017). metaSPAdes: a new versatile metagenomic assembler. Genome research, 27(5), 824-834. https://doi.org/10.1101/gr.213959.116 +- **Unicycler**: Wick, R.R., Judd, L.M., Gorrie, C.L. & Holt, K.E. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLOS Computational Biology 13, e1005595 (2017). https://doi.org/10.1371/journal.pcbi.1005595 - **MEGAHIT**: Li, D., Liu, C.-M., Luo, R., Sadakane, K. & Lam, T.-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674–1676 (2015). https://doi.org/10.1093/bioinformatics/btv033 ## Read mapping @@ -33,21 +33,21 @@ modules are added to aviary. ## Binning - **CONCOCT**: Alneberg, J. et al. Binning metagenomic contigs by coverage and composition. Nat Methods 11, 1144–1146 (2014). https://doi.org/10.1038/nmeth.3103 -- **VAMB**: Nissen, J. N. et al. Improved metagenome binning and assembly using deep variational autoencoders. Nature Biotechnology 1–6 (2021) doi:10.1038/s41587-020-00777-4. https://doi.org/10.1038/s41587-020-00777-4 -- **MetaBAT**: Kang, D. D., Froula, J., Egan, R. & Wang, Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 3, e1165 (2015). https://doi.org/10.7717/peerj.1165 -- **MetaBAT2**: Kang, D. D. et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7, (2019). https://doi.org/10.7717/peerj.7359 -- **DAS Tool**: Sieber, C. M. K. et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nature Microbiology 3, 836–843 (2018). https://doi.org/10.1038/s41564-018-0171-1 -- **SemiBin2**: Pan, S., Zhao, X. M., & Coelho, L. P. (2023). SemiBin2: self-supervised contrastive learning leads to better MAGs for short-and long-read sequencing, Bioinformatics, Volume 39, Issue Supplement_1, June 2023, Pages i21–i29. https://doi.org/10.1093/bioinformatics/btad209 -- **MaxBin 2.0**: Wu, Y.-W., Simmons, B. A. & Singer, S. W. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 32, 605–607 (2016). https://doi.org/10.1093/bioinformatics/btv638 +- **VAMB**: Nissen, J.N. et al. Improved metagenome binning and assembly using deep variational autoencoders. Nature Biotechnology 1–6 (2021) doi:10.1038/s41587-020-00777-4. https://doi.org/10.1038/s41587-020-00777-4 +- **MetaBAT**: Kang, D.D., Froula, J., Egan, R. & Wang, Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 3, e1165 (2015). https://doi.org/10.7717/peerj.1165 +- **MetaBAT2**: Kang, D.D. et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7, (2019). https://doi.org/10.7717/peerj.7359 +- **DAS Tool**: Sieber, C.M.K. et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nature Microbiology 3, 836–843 (2018). https://doi.org/10.1038/s41564-018-0171-1 +- **SemiBin2**: Pan, S., Zhao, X.M., & Coelho, L.P. (2023). SemiBin2: self-supervised contrastive learning leads to better MAGs for short-and long-read sequencing, Bioinformatics, Volume 39, Issue Supplement_1, June 2023, Pages i21–i29. https://doi.org/10.1093/bioinformatics/btad209 +- **MaxBin 2.0**: Wu, Y.-W., Simmons, B.A. & Singer, S.W. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 32, 605–607 (2016). https://doi.org/10.1093/bioinformatics/btv638 - **Rosella**: https://github.com/rhysnewell/rosella ## Annotation -- **CheckM2**: Chklovski, A., Parks, D. H., Woodcroft, B. J., & Tyson, G. W. (2023). CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nature Methods, 1-10. https://doi.org/10.1038/s41592-023-01940-w -- **CheckM**: Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015). https://doi.org/10.1101/gr.186072.114 -- **eggNOG mapper 2**: Cantalapiedra, C. P., Hernández-Plaza, A., Letunic, I., Bork, P., & Huerta-Cepas, J. (2021). eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Molecular biology and evolution, 38(12), 5825-5829. https://doi.org/10.1093/molbev/msab293 -- **GTDB-Tk 2**: Chaumeil, P. A., Mussig, A. J., Hugenholtz, P., & Parks, D. H. (2022). GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics, 38(23), 5315-5316. https://doi.org/10.1093/bioinformatics/btac672 -- **GraftM**: Boyd, J. A., Woodcroft, B. J. & Tyson, G. W. GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes. Nucleic Acids Research 46, e59 (2018). https://doi.org/10.1093/nar/gky174 -- **CoverM**: Woodcroft B.J., Newell. R.J.P., Aroney S. T. N., Nissen J., Carmago A., Tyson G.W. CoverM: Read mapping statistics for metagenomics. Available at https://github.com/wwood/CoverM +- **CheckM2**: Chklovski, A., Parks, D.H., Woodcroft, B.J., & Tyson, G.W. (2023). CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nature Methods, 1-10. https://doi.org/10.1038/s41592-023-01940-w +- **CheckM**: Parks, D.H., Imelfort, M., Skennerton, C.T., Hugenholtz, P. & Tyson, G.W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015). https://doi.org/10.1101/gr.186072.114 +- **eggNOG mapper 2**: Cantalapiedra, C.P., Hernández-Plaza, A., Letunic, I., Bork, P., & Huerta-Cepas, J. (2021). eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Molecular biology and evolution, 38(12), 5825-5829. https://doi.org/10.1093/molbev/msab293 +- **GTDB-Tk 2**: Chaumeil, P.A., Mussig, A.J., Hugenholtz, P., & Parks, D.H. (2022). GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics, 38(23), 5315-5316. https://doi.org/10.1093/bioinformatics/btac672 +- **GraftM**: Boyd, J.A., Woodcroft, B.J. & Tyson, G.W. GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes. Nucleic Acids Research 46, e59 (2018). https://doi.org/10.1093/nar/gky174 +- **CoverM**: Woodcroft B.J., Newell. R.J.P., Aroney S.T.N., Nissen J., Carmago A., Tyson G.W. CoverM: Read mapping statistics for metagenomics. Available at https://github.com/wwood/CoverM ## Variant calling - **Lorikeet**: Newell R.J.P., McMaster E.S., Craig P., Boden M., Tyson G.W., Woodcroft B.J. Available at https://github.com/rhysnewell/Lorikeet From bd4b3e7810b6f6ee29839dbf358f4513d2c5eba1 Mon Sep 17 00:00:00 2001 From: Rhys Newell Date: Mon, 20 Nov 2023 11:45:05 +1100 Subject: [PATCH 7/7] fix: update rosella citation --- docs/citations.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/citations.md b/docs/citations.md index 1bd55021..3d3a38d6 100755 --- a/docs/citations.md +++ b/docs/citations.md @@ -39,7 +39,7 @@ modules are added to aviary. - **DAS Tool**: Sieber, C.M.K. et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nature Microbiology 3, 836–843 (2018). https://doi.org/10.1038/s41564-018-0171-1 - **SemiBin2**: Pan, S., Zhao, X.M., & Coelho, L.P. (2023). SemiBin2: self-supervised contrastive learning leads to better MAGs for short-and long-read sequencing, Bioinformatics, Volume 39, Issue Supplement_1, June 2023, Pages i21–i29. https://doi.org/10.1093/bioinformatics/btad209 - **MaxBin 2.0**: Wu, Y.-W., Simmons, B.A. & Singer, S.W. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 32, 605–607 (2016). https://doi.org/10.1093/bioinformatics/btv638 -- **Rosella**: https://github.com/rhysnewell/rosella +- **Rosella**: Newell, R. J. P., Tyson, G. W., & Woodcroft, B. J. (2023). Rosella: Metagenomic binning using UMAP and HDBSCAN. Available at https://github.com/rhysnewell/rosella ## Annotation - **CheckM2**: Chklovski, A., Parks, D.H., Woodcroft, B.J., & Tyson, G.W. (2023). CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nature Methods, 1-10. https://doi.org/10.1038/s41592-023-01940-w