Assembling a plant genome is challenging due to the abundance of repetitive sequences,
yet no standard is available to evaluate the assembly of repeat space. LTR retrotransposons …

Motivation The emergence of high-throughput sequencing technologies revolutionized
genomics in early 2000s. The next revolution came with the era of long-read sequencing …

Annotation of plant genomes is still a challenging task due to the abundance of repetitive
sequences, especially long terminal repeat (LTR) retrotransposons. LTR_FINDER is a …

Motivation: For most research approaches, genome analyses are dependent on the
existence of a high quality genome reference assembly. However, the local accuracy of an …

Transcriptomic sequence resources represent invaluable assets for research, in particular
for non-model species without a sequenced genome. To date, the Next Generation …

The commercial release of third-generation sequencing technologies (TGSTs), giving long
and ultra-long sequencing reads, has stimulated the development of new tools for …

Background Completing a genome is an important goal of genome assembly. However,
many assemblies, including reference assemblies, are unfinished and have a number of …

Background The development of next-generation sequencing has made it possible to
sequence whole genomes at a relatively low cost. However, de novo genome assemblies …

Background The advent of third-generation sequencing (TGS) technologies opens the door
to improve genome assembly. Long reads are promising for enhancing the quality of …

Sequence assembly of large and repeat-rich plant genomes has been challenging,
requiring substantial computational resources and often several complementary sequence …