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Heng Li 2018-02-15 17:21:09 -05:00
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27
README.md
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@ -38,7 +38,7 @@ man ./minimap2.1
- [Advanced features](#advanced) - [Advanced features](#advanced)
- [Working with >65535 CIGAR operations](#long-cigar) - [Working with >65535 CIGAR operations](#long-cigar)
- [The cs optional tag](#cs) - [The cs optional tag](#cs)
- [Evaluation scripts](#eval) - [Working with the PAF format](#paftools)
- [Algorithm overview](#algo) - [Algorithm overview](#algo)
- [Getting help](#help) - [Getting help](#help)
- [Citing minimap2](#cite) - [Citing minimap2](#cite)
@ -256,26 +256,13 @@ the alignment. The above example will become
`=CGATCG-ata=AATAGAGTAG+gtc=GAAT*at=GCA`. The long form of `cs` encodes both `=CGATCG-ata=AATAGAGTAG+gtc=GAAT*at=GCA`. The long form of `cs` encodes both
reference and query sequences in one string. reference and query sequences in one string.
#### <a name="eval"></a>Evaluation scripts #### <a name="paftools"></a>Working with the PAF format
Minimap2 comes with several (java)scripts for evaluating the accuracy of Minimap2 also comes with a (java)script [paftools.js](misc/paftools.js) that
minimap2. These scripts require the [k8][k8] javascript shell to run. processes alignments in the PAF format. It calls variants from
Recent minimap2 binary release tar-balls contain a copy of k8 executable, a assembly-to-reference alignment, lifts over BED files based on alignment,
single file. Here are a few examples on how to use these scripts: converts between formats and provides utilities for various evaluations. For
details, please see [misc/README.md](misc/README.md).
```sh
# Generate reads from PBSIM alignment (truth encoded in read names)
k8 misc/sim-pbsim.js ref.fa.fai pbsim-aln.maf > pbsim-reads.fq
# Generate reads from mason2 alignment (not tested for simulated SVs)
k8 misc/sim-mason2.js mason2-aln.sam > mason2-reads.fq
# Evaluate mapping accuracy with ROC-like curve
k8 misc/sim-eval.js my-aln.sam.gz > result.txt
k8 misc/sim-eval.js my-aln.paf.gz > result.txt
# Collect alignment statistics
k8 misc/mapstat.js my-aln.sam > result.txt
# Compare spliced junctions to existing gene annotations
k8 misc/intron-eval.js anno.gtf my-spliced-aln.sam > result.txt
```
### <a name="algo"></a>Algorithm overview ### <a name="algo"></a>Algorithm overview

21
minimap2.1
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@ -271,11 +271,22 @@ Cost for a non-canonical GT-AG splicing (effective with
.BR --splice ) .BR --splice )
[0] [0]
.TP .TP
.BI -z \ INT .BI -z \ INT1[,INT2]
Break an alignment if the running score drops too quickly along the diagonal of Truncate an alignment if the running alignment score drops too quickly along
the DP matrix (diagonal X-drop, or Z-drop) [400]. Increasing the value improves the diagonal of the DP matrix (diagonal X-drop, or Z-drop) [400,200]. If the
the contiguity of the alignment at the cost of poor alignment in the middle drop of score is above
(e.g. caused by a long inversion). .IR INT2 ,
minimap2 will reverse complement the query in the related region and align
again to test small inversions. Minimap2 truncates alignment if there is an
inversion or the drop of score is greater than
.IR INT1 .
Decrease
.I INT2
to find small inversions at the cost of performance and false positives.
Increase
.I INT1
to improves the contiguity of alignment at the cost of poor alignment in the
middle.
.TP .TP
.BI -s \ INT .BI -s \ INT
Minimal peak DP alignment score to output [40]. The peak score is computed from Minimal peak DP alignment score to output [40]. The peak score is computed from