Chromosome-level genome assembly and annotation of the loquat (Eriobotrya japonica) genome

Chromosome-level genome assembly and annotation of the loquat (Eriobotrya japonica) genome

(2020) Shuang Jiang et al.   GigaScience

Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi

(2018) Jens Keilwagen et al.   BMC BIOINFORMATICS

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

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

(2017) Sergey Koren et al.   GENOME RESEARCH

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Identification of protein coding regions in RNA transcripts

(2015) Shiyuyun Tang et al.   NUCLEIC ACIDS RESEARCH

PASTEC: An Automatic Transposable Element Classification Tool

(2014) Claire Hoede et al.   PLoS One

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

Expanded phylogenetic and dating analyses of the apples and their relatives (Pyreae, Rosaceae)

(2012) Eugenia Y.Y. Lo et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY