RepLong: de novo repeat identification using long read sequencing data

Abstract

Supplementary data are available at Bioinformatics online.

DeviaTE: Assembly‐free analysis and visualization of mobile genetic element composition

“…They may broadly be classified into approaches that require a genome assembly (e.g., RepeatMasker [Smit et al., 1996‐2010], PoPoolationTE2 [Kofler, Gómez‐Sánchez, & Schlötterer, ]) and approaches that do not require an assembled genome. The latter category can be further divided into tools that perform a de novo assembly of reads (e.g., RepeatExplorer [Novák, Neumann, Pech, Steinhaisl, & Macas, ], dnaPipeTE [Goubert et al., ], RepLong [Guo et al., ]) and tools that align reads to TE sequences (e.g., DeviaTE; Table ). These tools have different strengths and weaknesses.…”

“…However, if the sequence of a specific TE can not be found in any database, multiple tools for generating consensus sequences are available, e.g., RepARK, REPdenovo, RepeatScout, or RepLong (Chu, Pei, & Wu, 2018;Guo et al, 2017;Koch, Platzer, & Downie, 2014;Price, Jones, & Pevzner, 2005). These tools construct prototype sequences of repetitive elements from sequencing reads by assembling high-frequency repeat k-mers.…”

“…At a moderate divergence (<10%) the allele frequency is reproduced faithfully TA B L E 1 Comparison of different tools for analyzing TE abundance. The required input, the resulting output, notable features and shortcomings are shown for each tool (RepeatMasker [Smit et al, 1996[Smit et al, -2010 RepeatExplorer [Novák et al, 2013], dnaPipeTE [Goubert et al, 2015], RepLong [Guo et al, 2017] (adj. r 2 = 0.99 for 100 bp reads, adj.…”

“…RepLong [Guo et al, 2017]) and tools that align reads to TE sequences (e.g., DeviaTE; Table 1). These tools have different strengths and weaknesses.…”

RepAHR: an improved approach for de novo repeat identification by assembly of the high-frequency reads

“…MixTaR [ 9 ] firstly detects raw tandem repeat patterns from short reads, then selects out long reads containing raw tandem repeat patterns, and finally regards the assembly of the short reads which overlap long reads as TR repeats. RepLong [ 10 ] creates a read overlap network and uses community detection algorithm to detect long repeats by using only Pacbio long reads. REPdenovo [ 11 ] counts k-mer frequency and assembles k-mer into raw contigs, then merges contigs from directed contig graph into scaffolds to obtain repeats.…”