BleTIES: annotation of natural genome editing in ciliates using long read sequencing

Abstract

Summary: Ciliates are single-celled eukaryotes that eliminate specific, interspersed DNA sequences (internally eliminated sequences, IESs) from their genomes during development. These are challenging to annotate and assemble because IES-containing sequences are typically much less abundant in the cell than those without, and IES sequences themselves often contain repetitive and low-complexity sequences. Long-read sequencing technologies from Pacific Biosciences and Oxford Nanopore have the potential to reconstruct longer IESs than has been possible with short reads but require a different assembly strategy. Here we present BleTIES, a software toolkit for detecting, assembling, and analyzing IESs using mapped long reads.

Availability and implementation: BleTIES is implemented in Python 3. Source code is available at https://github.com/Swart-lab/bleties (MIT license) and also distributed via Bioconda.

Supplementary information: Supplementary data are available at Bioinformatics online.

Fig. 1.

Overview of BleTIES MILRAA method to reconstruct IES junctions from error-corrected CCS reads versus from subreads. (A) CCS reads have accuracy >99%, so the consensus insert coordinate from read mapping is adequate if coverage is sufficient. (B) (1) Subreads have higher error rates, so mapping alone is insufficient to define the insert position. (2) Therefore, clusters of adjacent inserts are identified, from which the insert sequence plus flanking ±100 bp are extracted from the subreads. (3) Extracted sequences are assembled with SPOA (Vaser et al., 2017). (4 and 5) This consensus is realigned to the reference to obtain a more accurate estimate of the insert position