From contigs towards chromosomes: automatic improvement of long read assemblies (ILRA).

ABSTRACT: Recent advances in long read technologies not only enable large consortia to aim to sequence all eukaryotes on Earth, but they also allow individual laboratories to sequence their species of interest with relatively low investment. Long read technologies embody the promise of overcoming scaffolding problems associated with repeats and low complexity sequences, but the number of contigs often far exceeds the number of chromosomes and they may contain many insertion and deletion errors around homopolymer tracts. To overcome these issues, we have implemented the ILRA pipeline to correct long read-based assemblies. Contigs are first reordered, renamed, merged, circularized, or filtered if erroneous or contaminated. Illumina short reads are used subsequently to correct homopolymer errors. We su

SUBMITTER: Ruiz JL 

PROVIDER: S-EPMC10359078 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature