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Questions tagged [minimap2]

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Extracting positions from PAF files in order to extract sequences from a Fastq file with Python

I have used Minimap2 to create a paf file by aligning a Fastq file against itself. Now from this Paf file I can see where the reads overlap, and I want to take these positions, and use them to extract ...
Newprogrammer's user avatar
0 votes
1 answer
60 views

Is my reference sequence too small?

I'm trying to map ONT long reads to a portion of a gene I'm looking at. The region is about 25bp long. When I search for the region in the document it pulls up the sequence in every read but when I ...
rimo's user avatar
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1 vote
1 answer
156 views

Nextflow with Minimap2 not working

I'm trying to create a Nextflow script that maps assemblies to reference gene sequences. This is what I have so far: ...
rimo's user avatar
  • 494
2 votes
1 answer
343 views

Understanding PAF format

Does anyone have any experience with PAF files (minimap2 output)? I don’t fully understand what my output means. I’ve looked at the minimap2 explanation (https://github.com/lh3/miniasm/blob/master/PAF....
rimo's user avatar
  • 494
2 votes
1 answer
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Get number of reads with a single, (almost) exact match to the full length of a reference sequence

I can't find an answer to this in previous questions, so hoping someone can help me now. We have nanopore sequenced a PCR product, and I've filtered our reads to +/- 10 bp of the expected product ...
Nat R McB's user avatar
2 votes
2 answers
111 views

Minimap2 detects too many 16S sequences in metagenome

I'd like to extract bacterial sequences from a metagenome where ~99% of contigs are from a host insect. My current protocol minimaps every 16S sequences present in the sample, then blasts all those ...
schmiggle's user avatar
1 vote
1 answer
76 views

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

I have a contigs file that I generated using Minia and then I have used Minimap2 to map these contigs again to the reference genome. Now I want to plot the gap distribution i.e. gap distance of the ...
my_new_user's user avatar
2 votes
2 answers
3k views

How do you visualize minimap2's PAF output format?

As described by the developer of minimap2: PAF is a text format describing the approximate mapping positions between two set of sequences. He also suggest to use either Ribbon to visualize PAF files,...
0x90's user avatar
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1 vote
1 answer
1k views

Why index a sequence file with minimap2?

I have been using minimap2 for a few month now and I just found a script that follows these steps: ...
Paul Endymion's user avatar
2 votes
1 answer
436 views

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

Heng Li's paper on minimap2 is understandable to me right up until the moment that it gives this definition of gap cost: 2.2.1 Alignment with 2-piece affine gap cost Minimap2 performs DP-based ...
Mark Amery's user avatar
3 votes
1 answer
2k views

Convert PAF format to SAM/BAM format

I have a bunch of PAF files resulting from the alignments of fastq files on a reference genome with minimap2. I would like to convert them into SAM/BAM format so I can use ...
Paul Endymion's user avatar
4 votes
2 answers
395 views

Mapping Reads to Known Gene Paralogs with Long Read Technology

I have some sequencing data from a captured region that is a known paralog edited. For now, I have been mapping the data using standard minimap2 flags for PacBio DNA sequencing: ...
d_kennetz's user avatar
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4 votes
1 answer
242 views

Error correction within the long read

I am going to get some data from plasmid sequencing to identify SNPs on the plasmids. What is done in the lab is the following: The plasmids are purified by size. We amplify the plasmids using the ...
Praderas's user avatar
  • 143
3 votes
2 answers
374 views

How to map reads shorter than 32bp with minimap2?

I mapped fasta sequences to a reference. The fasta sequences range in length from 17bp up to several hundred bp. I used minimap2 with the following command: ...
conchoecia's user avatar
  • 3,111
2 votes
1 answer
208 views

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

I have used minimap2 to map some pacbio reads to a reference genome. I would like to know the "insert size" (true length of sequence) relative to the reference. More specifically, I want to know the ...
conchoecia's user avatar
  • 3,111