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6 votes
Accepted

Why index a sequence file with minimap2?

If you don't provide an index, minimap2 will just generate the index on the fly (so, yes, it's done without specifying it). As such the mapping step will take longer. However, index generation is ...
DavyCats's user avatar
  • 497
5 votes
Accepted

Why are Minimap2 alignments different with CIGAR generation flag?

The program's author pointed me to the Minimap2 FAQ: 1. Alignment different with option -a or -c? Without ...
Gawain's user avatar
  • 315
5 votes
Accepted

Understanding PAF format

As @user172818 mentioned in a comment to your question, it looks like you might have used the query as the reference; they should be switched round. A minimap2 mapping command is typically represented ...
5 votes

What do the symbols mean in minimap2's gap cost equation?

Here is the translation: $l$ = gap length $q$ = initial gap penalty for shorter gaps $e$ = short gap extension penalty per every additional gap $\tilde{q}$ = initial gap penalty for longer gaps $\...
Eric Leung's user avatar
5 votes

How do you visualize minimap2's PAF output format?

As described in the minimap2 manual, -x STR is used to specify a preset option like -x map-pb for ...
vkkodali's user avatar
  • 1,266
4 votes

How do you visualize minimap2's PAF output format?

Depending on what level of information you need, it is not difficult to just homebrew a plot in your plotting package of choice, as PAF has relevant coordinate information. Unless you are interested ...
Maximilian Press's user avatar
4 votes

Nextflow with Minimap2 not working

Command error: .command.sh: line 2: ./minimap2: No such file or directory Work dir: /Users/rimo/Desktop/AWS/minimap2/work/ae/47e3c0708f33b1949315fc83066b95 ...
Steve's user avatar
  • 3,109
3 votes

Minimap2 detects too many 16S sequences in metagenome

16S is a very conserved sequence, which is why it's used for targeted phylogenetic analysis; it makes it easy to amplify and analyse. Unfortunately that conservation is an issue with minimap2, which ...
gringer's user avatar
  • 14.3k
3 votes

Is my reference sequence too small?

That's not the right way to do it. You either have reference or not. If not, you need to assemble one (that problem is called genome assembly). If yes, you map all the reads to the whole reference - ...
Kamil S Jaron's user avatar
3 votes

How to map reads shorter than 32bp with minimap2?

Minimap2 doesn't work well with 32bp reads by design. Older mappers like bowtie1 and bwa-aln will be better.
user172818's user avatar
  • 6,535
3 votes
Accepted

Mapping Reads to Known Gene Paralogs with Long Read Technology

Question 1 This command will get you all of supplementary alignments for the reads. This isn't exactly what you want though. You want all of the reads that have more than one mapping. ...
conchoecia's user avatar
  • 3,181
2 votes

Convert PAF format to SAM/BAM format

The paf format does not have the CIGAR string and base quality information that are typically present in a BAM/SAM file. While it is in principle possible to write a paf2sam converter, it's going to ...
KT8's user avatar
  • 81
2 votes
Accepted

Error correction within the long read

Yes, there is a tool to do this called R2C2 by the Vollmers lab at UC Santa Cruz. https://www.biorxiv.org/content/early/2018/06/04/338020
conchoecia's user avatar
  • 3,181
2 votes
Accepted

How to map reads shorter than 32bp with minimap2?

Minimap2 is not the most optimal aligner in this case, it was designed for long reads, of which 32bp reads are clearly not. You could try lowering the mnimizer k-mer length and with ...
Matt Bashton's user avatar
  • 1,069
2 votes
Accepted

Minimap2 -ax map-pb doesn't output tlen field

The TLEN for single-end reads is defined as 0 in the SAM specification, which is why this happens. You can still get the end position of the alignment by parsing the CIGAR string. An example using the ...
Devon Ryan's user avatar
  • 19.6k
2 votes
Accepted

Parameter optimisation of minimap2

First of all, use short read option The short read preset (-x sr) for minimap2 is heavily recommended for doing such mapping: ...
Maximilian Press's user avatar
2 votes

Minimap2 detects too many 16S sequences in metagenome

You are taking reads as the reference. Given the similarity of 16S, you will find hits for most 16S in other species. You have to filter out poor hits. This is the faster way if you don't have many ...
user172818's user avatar
  • 6,535
2 votes

How to plot the gap distribution of contigs wrt to reference genome

a better solution I wasn't too happy with the previous answer that I gave, so I was fiddling around, and I realized that bedtools genomecov will give you this for ...
Maximilian Press's user avatar
1 vote

Parameter optimisation of minimap2

Just to follow-up on the performance of minimap2: the solution @MaximillianPress described works. Thousands of hits are obtained for comparatively obscure genes (some will be duplicates). ...
M__'s user avatar
  • 12.5k
1 vote

Get number of reads with a single, (almost) exact match to the full length of a reference sequence

Because minimap2 is a minimiser-based mapper, it's less useful for determining mapping accuracy to single-base precision. Where precision matters, you can use LAST, bearing in mind that it calculates ...
gringer's user avatar
  • 14.3k

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