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Pauli Virtanen et al.
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ganon: precise metagenomics classification against large and up-to-date sets of reference sequences
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M. R. Wilson et al.
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MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples
Nathan LaPierre et al.
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Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
Daehwan Kim et al.
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rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data
Elena Bushmanova et al.
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The Pfam protein families database in 2019
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Pest categorisation of non-EU viruses and viroids of Cydonia Mill., Malus Mill. and Pyrus L.
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Clustal Omega for making accurate alignments of many protein sequences
Fabian Sievers et al.
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Minimap2: pairwise alignment for nucleotide sequences
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NanoPack: visualizing and processing long-read sequencing data
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Shifu Chen et al.
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Nanopore-based detection and characterization of yam viruses
Denis Filloux et al.
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KrakenUniq: confident and fast metagenomics classification using unique k-mer counts
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Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
Robert M. Bowers et al.
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MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
Martin Steinegger et al.
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Susan Jones et al.
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VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
Jie Ren et al.
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MetaCache: context-aware classification of metagenomic reads using minhashing
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Jaime Huerta-Cepas et al.
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MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
Dinghua Li et al.
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CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers
Rachid Ounit et al.
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VirSorter: mining viral signal from microbial genomic data
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Fast and sensitive protein alignment using DIAMOND
Benjamin Buchfink et al.
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Muhammad Tariq Pervez et al.
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Peter Skewes-Cox et al.
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Development of a virus detection and discovery pipeline using next generation sequencing
Thien Ho et al.
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Julia Dubois et al.
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Kazutaka Katoh et al.
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De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
Brian J. Haas et al.
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CD-HIT: accelerated for clustering the next-generation sequencing data
Limin Fu et al.
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Andrew E. Firth et al.
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Accelerated Profile HMM Searches
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Prodigal: prokaryotic gene recognition and translation initiation site identification
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BLAST plus : architecture and applications
Christiam Camacho et al.
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Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology
Ian P. Adams et al.
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Clustal W and clustal X version 2.0
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Translational control in positive strand RNA plant viruses
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MAFFT version 5: improvement in accuracy of multiple sequence alignment
K Katoh et al.
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MUSCLE: multiple sequence alignment with high accuracy and high throughput
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Pushing the limits of the scanning mechanism for initiation of translation
M Kozak
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An efficient algorithm for large-scale detection of protein families
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