<![CDATA[BOL: CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes]]> https://bioinformaticsonline.com/bookmarks/view/42941/csa-a-high-throughput-chromosome-scale-assembly-pipeline-for-vertebrate-genomes? https://bioinformaticsonline.com/bookmarks/view/42941/csa-a-high-throughput-chromosome-scale-assembly-pipeline-for-vertebrate-genomes Wed, 10 Mar 2021 06:13:49 -0600 https://bioinformaticsonline.com/bookmarks/view/42941/csa-a-high-throughput-chromosome-scale-assembly-pipeline-for-vertebrate-genomes <![CDATA[CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes]]> The pipeline can use information from scaffolded assemblies (for example from HiC or 10X Genomics), or even from diverged (~65-100 Mya) reference genomes for ordering the contigs and thus support the assembly process. This typically results in improved contig N50 when compared to current state of the art methods.

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For smaller vertebrate genomes (~1 Gbp) chromosome scale assemblies can be achieved within 12h on high-end Desktop computers (Intel i7, 12 CPU threads, 128 GB RAM). Larger mammalian genomes (~3Gbp) can be processed within 15-18 h on server equipment (Xeon, 96 CPU threads, 1TB RAM).

Address of the bookmark: https://github.com/HMPNK/CSA2.6

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