Closed camillescott closed 4 years ago
Primary annotation and configuration commands:
config
FASTA munging commands:
rename-fasta
transcriptome-stats
annotate-fasta
Filtering commands:
best-hits
Conversion commands:
maf-to-gff3
shmlast-to-gff3
hmmscan-to-gff3
cmscan-to-gff3
Transformation commands:
merge-gff3
remap-hmmer-coords
CLI Components
Primary annotation and configuration commands:
config
Show dammit configuration information.FASTA munging commands:
rename-fasta
Copy a FASTA file and rename the headers.transcriptome-stats
Run basic metrics on a transcriptomeannotate-fasta
Annotate a FASTA file from a GFF3 file.Filtering commands:
best-hits
Filter query best-hits from a MAF file.Conversion commands:
maf-to-gff3
Convert MAF to GFF3.shmlast-to-gff3
Convert shmlast CSV output to GFF3.hmmscan-to-gff3
Convert HMMER to GFF3.cmscan-to-gff3
Convert Infernal's cmscan output to GFF3.Transformation commands:
merge-gff3
Merge a collection of GFF3 files.remap-hmmer-coords
Remap hmmscan coordinates using TransDecoder ORF...