Issues

• Load custom genomes in addition/instead of NCBI

  hermidalc/dragonfish#25 · Filter by author hermidalc opened on Oct 29, 2022

• Add known human contaminant sequences in microbe genomes to decoys or host filtering steps

  enhancement
  hermidalc/dragonfish#24 · Filter by author hermidalc opened on Oct 19, 2022

• Finish SLURM setup so that workflow can get submitted to different nodes instead of running on one large node

  enhancement
  hermidalc/dragonfish#23 · Filter by author hermidalc opened on Oct 16, 2022

• Functionality to automatically collapse functional terms to larger pathways and associated read counts for appropriate functional DBs (i.e. GO, EC)

  enhancement
  hermidalc/dragonfish#22 · Filter by author hermidalc opened on Oct 16, 2022

• Input read host and decontaminant sequence filtering with HISAT2 (DNA, RNA) and STAR (RNA)

  enhancement
  hermidalc/dragonfish#21 · Filter by author hermidalc opened on Oct 6, 2022

• Use tximport-like approach to summarize Cedar abundance by functional ID

  enhancement
  hermidalc/dragonfish#19 · Filter by author hermidalc opened on Jul 10, 2022
  

• Cedar EM uncertainty/confidence scores

  enhancement
  hermidalc/dragonfish#17 · Filter by author hermidalc opened on Jul 10, 2022

• Map and summarize BAM read counts per CDS protein ID to functional DB IDs

  enhancement
  hermidalc/dragonfish#15 · Filter by author hermidalc opened on Jul 10, 2022 · 0.1
  

• Input RNA-seq ribosomal and structural RNA filtering (e.g. with SILVA)

  enhancement
  hermidalc/dragonfish#6 · Filter by author hermidalc opened on Jul 10, 2022