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1. nextseq_illumina nextseq_illuminaPublic

   Scripts for automated FASTq file upload to basespace from Illumina NGS machines (e.g. NextSeq 2000)

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2. gridion_ont gridion_ontPublic

   Scripts for Basecalling on GridION Sequenicng machines from Oxford Nanopore

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3. local_genbankdb- local_genbankdb-Public

   Scripts to download GenBank records, extract taxonomy, gene sequences and create files for qiime2 taxonomic classification

   Shell

4. SeqTrim SeqTrimPublic

   Script for trimming sequences at 5' and 3' ends for qiime2 clusterization step

   R

5. get_taxonomy_lineage get_taxonomy_lineagePublic

   Script to download taxonomy info based on list of accession numbers

   Perl

6. bacannot bacannotPublic

   Forked from fmalmeida/bacannot

   Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.

   Nextflow