lh3 / miniprot

Align proteins to genomes with splicing and frameshift

https://lh3.github.io/miniprot/

lh3/miniprot Issues

Feature Request: --junc-bed, --junc-bonus parameters
Updated 12 days ago3
Can this be used as a replacement for MetaEuk's eukaryotic gene prediction capabilities?
Updated 18 days ago5
An error when looking for 200 proteins in a genome
Closed 18 days ago7
Aligning to distant homologues
Closed 18 days ago2
large chromosome alignment may have empty output
Updated 18 days ago
Homologous comparison resulted in an empty GFF file.
Closed 2 months ago
Different translation tables
Closed 7 months ago7
Use information from conserved introns
Updated 7 months ago2
out-of-memory error
Closed 2 years ago1
Inserted internal stop codons are not penalized
Closed 7 months ago2
Filter by alignment quality
Closed 7 months ago1
There is always an additional amino acid residue after the final stop codon of the protein sequence with --trans
Closed 7 months ago1
GFF3 output is malformed for stop_codon features
Closed 7 months ago1
Inconsistent use of operators in the cs tag?
Closed 7 months ago1
How to achieve higher sensitivity?
Updated 8 months ago3
A way to prefer closer exons in tandemly duplicated genes on the same strand
Closed 10 months ago1
Using miniprot to identify homologous transposable elements?
Updated a year ago
Compile error on AMD EPYC 7742
Closed a year ago1
Is it necessary to shield repetitive sequences?
Closed a year ago1
Chimeric alignments spanning multiple adjacent genes
Updated a year ago3
Information function --trans
Closed a year ago1
'Killed' message from index build
Closed a year ago3
miniprot do not include stop_codon in gtf file?
Closed a year ago1
Internal stop codons
Updated a year ago
Memory error
Closed 2 years ago5
duplicate and close variants of the same alignment in the output
Updated 2 years ago4
limiting max intron size leads to removal of intronless alignment
Closed 2 years ago8
Segmentation fault
Closed 2 years ago
Negative length for introns in cs:Z: tag
Updated 2 years ago4
Valid introns being reported as deletions
Closed 2 years ago7
typo on the man page?
Closed 2 years ago2
Very large number of large introns for a plant genome
Closed 2 years ago2
aligning to Oxford Nanopore simplex reads (Q16)
Closed 2 years ago1
deletion in GFF output
Closed 2 years ago1
How to get exon and UTR cordinates like GenomeThreader?
Closed 2 years ago3
Question: using Miniprot for searching small peptides
Updated 2 years ago
Missing option --gff-only in help
Closed 2 years ago1
conda for miniprot
Closed 2 years ago1
Installing minprot using conda
Closed 2 years ago1
gff rank calculation
Closed 2 years ago1
Filter out very long intron gene (max intron size)
Updated 2 years ago6
Use for prokaryotes?
Closed 2 years ago1
Using miniprot projections as evidence class in evidencemodeler
Closed 2 years ago5
ID filed in attributes
Closed 2 years ago1
Splice model
Closed 2 years ago3
-j for plants or fungi
Closed 2 years ago1
Indexing is much slower on fragmented assemblies
Closed 2 years ago9
Limit to reported alignments?
Closed 2 years ago1
-w option appears not to be implemented
Closed 2 years ago1
What do you mean mapped in Evaluation table?
Closed 2 years ago1