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Bio-Scripts

• • Jit@jit.aber

  

  Install grabseqs with conda !

  (JitMetaENV) ➜ JitMeta conda install grabseqs -c louiejtaylor -c bioconda -c conda-forge Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.

  1244 days ago

• • Jit@jit.aber

  

  Install fastqc using conda !

  (JitMetaENV) ➜ JitMeta conda install -c bioconda fastqc Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.

  1244 days ago

• • Jit@jit.aber

  

  Install trimmomatic using conda !

  (JitMetaENV) ➜ fastQC_out conda install -c bioconda trimmomatic Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.

  1244 days ago

• • Jit@jit.aber

  

  trimmomatic command !

  ...hred33 SRR5322499_1.fastq out.trimmed.fastq LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 Automatically using 1 threads Input Reads: 72875 Surviving: 72865 (99.99%) Dropped: 10...

  1244 days ago

• • Jit@jit.aber

  

  Install spades using conda !

  (JitMetaENV) ➜ fastQC_out conda install -c bioconda spades Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.

  1244 days ago

• • Jit@jit.aber

  

  Install assembly-stats with conda !

  (JitMetaENV) ➜ META_PE conda install -c bioconda assembly-stats Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.

  1244 days ago

• • Jit@jit.aber

  

  Install Kraken2 using conda !

  ...kraken2 Collecting package metadata (current_repodata.json): done Solving environment: failed with initial f...repodata source. Collecting package metadata (repodata.json): done Solving environment: done ==>...

  1243 days ago

• • Jit@jit.aber

  

  Install quast using conda !

  (JitMetaENV) ➜ ~ conda install -c bioconda quast Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exist...

  1243 days ago

• • Jit@jit.aber

  

  Install prokka using conda !

  ...a prokka Collecting package metadata (current_repodata.json): done Solving environment: failed with initial f...repodata source. Collecting package metadata (repodata.json): done Solving environment: done ==>...

  1243 days ago

• • Jit@jit.aber

  

  Install seqtk using conda !

  (JitMetaENV) ➜ META_PE conda install -c bioconda seqtk Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.

  1243 days ago

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