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Release 0.13-r248 (6 March 2024)

Notable changes:

  • New feature: added option -T to specify a non-standard NCBI translation table (#56 and #57). As this is an indexing option, the binary index format has to be changed accordingly. Miniprot will reject indices built with previous versions.

  • Improvement: properly handle reference deletions involving in-frame stop codons (#58). Older versions would not penalize these stop codons. This change also improves junction accuracy especially for distant homologs.

  • Bug fix: in the GFF3 output, CDS now includes stop codons (#55). Note the in GTF, CDS excludes stop codons.

  • Bug fix: suppress an extra amino acid in the --trans or --aln output (#47). In rare cases, this may lead to memory violation.

(0.13: 6 March 2024, r248)

Release 0.12-r237 (24 June 2023)

Notable changes:

  • New feature: added option --no-cs to disable the cs tag. This tag is not as useful as the cs tag for nucleotide alignment because it does not encode the matching amino acids.

  • New feature: output the number of frameshifts and in-frame stop codons in the PAF output. It is non-trivial to parse in-frame stop codons.

  • Bugfix: fixed malformatted protein sequences when --gtf and --trans are both specified (#45).

(0.12: 24 June 2023, r237)

Release 0.11-r234 (18 April 2023)

Notable changes:

  • New feature: added option --trans to output translated protein sequences. It is possible to extract these sequences from the --aln output but the --trans output is smaller and more convenient.

  • Bugfix: infinite error messages if a wrong option is in use.

  • Improvement: better error messages given nonexisting query files (#40).

(0.11: 18 April 2023, r234)

Release 0.10-r225 (3 April 2023)

Notable change:

  • Bugfix: rare segmentation fault (#38 and #39). This bug affected all previous versions of miniprot.

(0.10: 3 April 2023, r225)

Release 0.9-r223 (9 March 2023)

Notable change:

  • Bugfix: some query proteins were not outputted with option -u.

(0.9: 9 March 2023, r223)

Release 0.8-r220 (6 March 2023)

Notable changes:

  • Improvement: slightly improved the sensitivity to distant homolog at a minor cost of specificity. On the human-zebrafish dataset, we gained 1.2% junction sensivity at the cost of 0.2% of specificity.

  • New feature: added option --aln to output residue alignment.

  • New feature: added option -I to automatically set the maximum intron size to sqrt(GenomeSize) * 3.6, where GenomeSize is the total length of the nucleotide sequences. For smaller genomes, a smaller threshold leads to higher accuracy. This option is not the default because the reference is not always a genome.

(0.8: 6 March 2023, r220)

Release 0.7-r207 (25 December 2022)

Notable changes:

  • Improvement: replaced open syncmers with modimers. This simplifies the code and slightly reduces the memory at comparable k-mer sampling rate. This changes the index format.

  • Improvement: fine tune parameters for higher sensitivity at a minor cost of junction accuracy: a) only index ORFs >= 30bp; b) reduced max k-mer occurrences from 50k to 20k; c) sample k-mers at a rate of 50%; d) reduced min number of k-mers from 5 to 3; e) add a bonus chaining score for anchors on the same reference block.

  • Improvement: adjust the max k-mer occurrence dynamically per protein.

  • Improvement: implemented 2-level chaining like minimap2 and minigraph. This reduces chaining time.

  • Bugfix: fixed a rare off-by-1 memory violation

  • Bugfix: fixed a memory leak

Overall, miniprot becomes faster at slightly higher peak memory usage. It is more sensitive to distant homologs, though the junction accuracy of additional alignment is usually lower. Also importantly, the index format of miniprot has been changed. Miniprot will throw an error if you use miniprot with pre-built indices generated with older versions.

(0.7: 25 December 2022, r207)

Release 0.6-r185 (12 December 2022)

Notable changes:

  • Improvement: for each protein, only output alignments close to the best alignment. Also added option --outs to tune the threshold.

  • New feature: output GTF with option --gtf.

(0.6: 22 December 2022, r185)

Release 0.5-r179 (17 October 2022)

Notable changes:

  • Improvement: more detailed splice model considering G|GTR..YYYNYAG|. This is not enabled by default. Added option -j to change the splice model.

  • Added the miniprot preprint. Available at http://arxiv.org/abs/2210.08052

(0.5: 17 October 2022, r179)

Release 0.4-r165 (5 October 2022)

This version implements a better splice model and pays a little more effort in aligning terminal exons. It improves both sensitivity and specificity by a few percent.

Other notable changes:

  • Breaking change: changed -C to scale the splice model

  • Bugfix: implemented option -w (#12)

  • Bugfix: reduced the indexing time for highly fragmented genomes (#12)

  • New feature: output a Rank attribute in GFF

(0.4: 5 October 2022, r165)

Release 0.3-r137 (22 September 2022)

Notable changes:

  • Improvement: fine tune parameters and heuristics: higher non-GT-AG penalty, higher frameshift penalty, higher penalty on in-frame stop codons and a small penalty on long terminal introns. Miniprot is a little more sensitive and a little more accurate, at a minor cost of performance.

  • New feature: richer GFF output. Miniprot now reports per-exon alignment score, number of frameshifts, number of in-frame stop codons and non-canonical donor/acceptor sequences.

  • New feature: added option --outn to control the number of alignments per protein to output.

  • New feature: added option -P to change the ID prefix in GFF output (#6).

  • Bug fix: fixed a segmentation fault when there are no k-mers on a reference sequence (#4).

(0.3: 22 September 2022, r137)

Release 0.2-r116 (12 September 2022)

Notable changes:

  • New feature: output GFF3 with option --gff. PAF alignments are embedded in ##PAF lines in the output GFF3.

  • Improvement: give a bonus score -B if extension reaches the end of a protein. BWA-MEM and minimap2 both have this heuristic.

  • Improvement: pay more effort to the first and the last exons. This increases the sensitivity at the cost of performance.

  • Improvement: increased non-canonical splicing penalty -C from 6 to 11. This increases overall specificity.

  • Improvement: rank an alignment with the DP score disregarding introns. This is to reduce the effect pseudogenes. Minimap2 uses the same strategy.

  • Bug fixes: fixed incorrect CIGAR in corner cases and patched a minor memory leak.

This version works on several real datasets to decent accuracy without crashing or memory leaks. It is ready for more users.

(0.2: 12 September 2022, r116)

Release 0.1-r97 (9 September 2022)

This is the first public release of miniprot, a mapper for aligning proteins to a large genome. This release has a few issues and is generally not recommended for production uses.

(0.1: 9 September 2022, r97)