Benjamin Buchfink, Chao Xie, Daniel H Huson. Nat Methods 2015
Times Cited: 3590
Times Cited: 3590
Times Cited
Times Co-cited
Similarity
Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
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IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.
Lam-Tung Nguyen, Heiko A Schmidt, Arndt von Haeseler, Bui Quang Minh. Mol Biol Evol 2015
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Basic local alignment search tool.
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MAFFT multiple sequence alignment software version 7: improvements in performance and usability.
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The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.
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Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
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The Sequence Alignment/Map format and SAMtools.
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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
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MUSCLE: multiple sequence alignment with high accuracy and high throughput.
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Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
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OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy.
David M Emms, Steven Kelly. Genome Biol 2015
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Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.
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Fast and accurate short read alignment with Burrows-Wheeler transform.
Heng Li, Richard Durbin. Bioinformatics 2009
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Full-length transcriptome assembly from RNA-Seq data without a reference genome.
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StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.
Mihaela Pertea, Geo M Pertea, Corina M Antonescu, Tsung-Cheng Chang, Joshua T Mendell, Steven L Salzberg. Nat Biotechnol 2015
Mihaela Pertea, Geo M Pertea, Corina M Antonescu, Tsung-Cheng Chang, Joshua T Mendell, Steven L Salzberg. Nat Biotechnol 2015
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Fast and sensitive taxonomic classification for metagenomics with Kaiju.
Peter Menzel, Kim Lee Ng, Anders Krogh. Nat Commun 2016
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trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
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Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden. BMC Bioinformatics 2009
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GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database.
Pierre-Alain Chaumeil, Aaron J Mussig, Philip Hugenholtz, Donovan H Parks. Bioinformatics 2019
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CheckV assesses the quality and completeness of metagenome-assembled viral genomes.
Stephen Nayfach, Antonio Pedro Camargo, Frederik Schulz, Emiley Eloe-Fadrosh, Simon Roux, Nikos C Kyrpides. Nat Biotechnol 2021
Stephen Nayfach, Antonio Pedro Camargo, Frederik Schulz, Emiley Eloe-Fadrosh, Simon Roux, Nikos C Kyrpides. Nat Biotechnol 2021
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eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
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MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis.
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Improved metagenomic analysis with Kraken 2.
Derrick E Wood, Jennifer Lu, Ben Langmead. Genome Biol 2019
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fastp: an ultra-fast all-in-one FASTQ preprocessor.
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VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses.
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Interactive Tree Of Life (iTOL) v4: recent updates and new developments.
Ivica Letunic, Peer Bork. Nucleic Acids Res 2019
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ModelFinder: fast model selection for accurate phylogenetic estimates.
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High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries.
Chirag Jain, Luis M Rodriguez-R, Adam M Phillippy, Konstantinos T Konstantinidis, Srinivas Aluru. Nat Commun 2018
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FastTree 2--approximately maximum-likelihood trees for large alignments.
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eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.
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Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.
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MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities.
Dongwan D Kang, Jeff Froula, Rob Egan, Zhong Wang. PeerJ 2015
Dongwan D Kang, Jeff Froula, Rob Egan, Zhong Wang. PeerJ 2015
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Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.