Michael Grünstäudl (Gruenstaeudl), PhD

Postdoctoral Researcher at the Freie Universität Berlin

Monatsarchiv für August 2020

Automatically renaming contigs of assembly results

The genome assembly process often generates FASTA-formatted contig files, in which the contigs have cryptic sequence names. By using specific Bash commands, one can automatically rename these contigs based on the name of the file they are contained in. If your contig file contains only a single contig: for i in *__contig.fasta; do VAR=${i%__contig.fasta*}; sed […]

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