4.7 Article

Comparison of assembly platforms for the assembly of the nuclear genome of Trichoderma harzianum strain PAR3

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Search and sequence analysis tools services from EMBL-EBI in 2022

Fabio Madeira et al.

Summary: The EMBL-EBI search and sequence analysis tools frameworks allow integrated access to data resources and core bioinformatics analytical tools. These tools can be interacted with through user-friendly web applications and APIs. Recent improvements have been made to accommodate the increasing data requirements during the COVID-19 pandemic.

NUCLEIC ACIDS RESEARCH (2022)

Article Mycology

In honor of John Bissett: authoritative guidelines on molecular identification of Trichoderma

Feng Cai et al.

Summary: Modern taxonomy is moving towards establishing global authoritative lists of species, but in fungi, species delimitation is often subjective, which complicates accurate identification. The genus Trichoderma offers insights into the challenges of species identification and highlights the need for cooperation among researchers in handling upcoming genomic data.

FUNGAL DIVERSITY (2021)

Letter Biochemistry & Molecular Biology

BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

Mose Manni et al.

Summary: The BUSCO software provides essential methods for assessing the quality of genomic and metagenomic data, offering new functionalities and improvements to streamline the process. It is capable of evaluating both eukaryotic and prokaryotic species, and can be used across various data types including genome assemblies, metagenomic bins, transcriptomes, and gene sets.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Article Biochemistry & Molecular Biology

tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes

Patricia P. Chan et al.

Summary: tRNAscan-SE, a tool for predicting transfer RNA genes, has been widely used for over twenty years. Recent updates have greatly improved its ability to identify and classify tRNAs by creating nearly one hundred specialized isotype- and Glade-specific models.

NUCLEIC ACIDS RESEARCH (2021)

Article Multidisciplinary Sciences

RepeatModeler2 for automated genomic discovery of transposable element families

Jullien M. Flynn et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Multidisciplinary Sciences

Highly accurate long-read HiFi sequencing data for five complex genomes

Ting Hon et al.

SCIENTIFIC DATA (2020)

Article Biotechnology & Applied Microbiology

Assembly of long, error-prone reads using repeat graphs

Mikhail Kolmogorov et al.

NATURE BIOTECHNOLOGY (2019)

Article Biochemistry & Molecular Biology

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

Kai Blin et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biotechnology & Applied Microbiology

Evolution and comparative genomics of the most common Trichoderma species

Christian P. Kubicek et al.

BMC GENOMICS (2019)

Article Biochemistry & Molecular Biology

Genome-based estimates of fungal rDNA copy number variation across phylogenetic scales and ecological lifestyles

Lotus A. Lofgren et al.

MOLECULAR ECOLOGY (2019)

Article Biochemical Research Methods

Versatile genome assembly evaluation with QUAST-LG

Alla Mikheenko et al.

BIOINFORMATICS (2018)

Article Biochemistry & Molecular Biology

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

Sudhir Kumar et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Biochemistry & Molecular Biology

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

Sergey Koren et al.

GENOME RESEARCH (2017)

Review Biotechnology & Applied Microbiology

Trichoderma for climate resilient agriculture

Prem Lal Kashyap et al.

WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY (2017)

Article Biochemical Research Methods

HYBRIDSPADES: an algorithm for hybrid assembly of short and long reads

Dmitry Antipov et al.

BIOINFORMATICS (2016)

Article Biochemical Research Methods

InterProScan 5: genome-scale protein function classification

Philip Jones et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

The MaSuRCA genome assembler

Aleksey V. Zimin et al.

BIOINFORMATICS (2013)

Review Agronomy

Grapevine trunk diseases: complex and still poorly understood

C. Bertsch et al.

PLANT PATHOLOGY (2013)

Review Biotechnology & Applied Microbiology

β-Glucosidases from the Fungus Trichoderma: An Efficient Cellulase Machinery in Biotechnological Applications

Pragya Tiwari et al.

BIOMED RESEARCH INTERNATIONAL (2013)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

Mario Stanke et al.

BIOINFORMATICS (2008)

Article Biochemistry & Molecular Biology

MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes

Brandi L. Cantarel et al.

GENOME RESEARCH (2008)

Article Biochemical Research Methods

Gene finding in novel genomes

I Korf

BMC BIOINFORMATICS (2004)