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Load custom genomes in addition/instead of NCBI

Status: Open.

#25 In hermidalc/dragonfish;

· hermidalc opened on Oct 29, 2022

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

enhancementNew feature or requestNew feature or request

Status: Open.

#24 In hermidalc/dragonfish;

· 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

enhancementNew feature or requestNew feature or request

Status: Open.

#23 In hermidalc/dragonfish;

· 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)

enhancementNew feature or requestNew feature or request

Status: Open.

#22 In hermidalc/dragonfish;

· hermidalc opened on Oct 16, 2022

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

enhancementNew feature or requestNew feature or request

Status: Open.

#21 In hermidalc/dragonfish;

· hermidalc opened on Oct 6, 2022

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

enhancementNew feature or requestNew feature or request

Status: Open.

#19 In hermidalc/dragonfish;

· hermidalc opened on Jul 10, 2022

Cedar EM uncertainty/confidence scores

enhancementNew feature or requestNew feature or request

Status: Open.

#17 In hermidalc/dragonfish;

· hermidalc opened on Jul 10, 2022

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

enhancementNew feature or requestNew feature or request

Status: Open.

#15 In hermidalc/dragonfish;

· hermidalc opened on Jul 10, 2022

·  

0.1

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

enhancementNew feature or requestNew feature or request

Status: Open.

#6 In hermidalc/dragonfish;

· hermidalc opened on Jul 10, 2022