Slag: A program for seeded local assembly of genes in complex genomes.

ABSTRACT: Although finished genomes have become more common, there is still a need for assemblies of individual genes or chromosomal regions when only unassembled reads are available. slag (Seeded Local Assembly of Genes) fulfils this need by performing iterative local assembly based on cycles of matching-read retrieval with blast and assembly with cap3, phrap, spades, canu or unicycler. The target sequence can be nucleotide or protein. Read fragmentation allows slag to use phrap or cap3 to assemble long reads at lower coverage (e.g., 5×) than is possible with canu or unicycler. In simple, nonrepetitive genomes, a slag assembly can cover a whole chromosome, but in complex genomes the growth of target-matching contigs is limited as additional reads are consumed by consensus contigs consisting of repe

SUBMITTER: Crane CF 

PROVIDER: S-EPMC9303413 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature