20 votes
Accepted

Read length distribution from FASTA file

If you want something quick and dirty you could rapidly index the FASTA with samtools faidx and then put the lengths column through R (other languages are available)...
user avatar
12 votes

Read length distribution from FASTA file

Statistics for nanopore reads are tricky because of the huge range of read lengths that can be present in a single run. I have found that the best way to display lengths is by using a log scale on ...
user avatar
  • 11.5k
11 votes
Accepted

Tools for simulating Oxford Nanopore reads

Simulators designed specifically for Oxford Nanopore: NanoSim NanoSim-H SiLiCO ReadSim DeepSimulator General long read simulators: Loresim Loresim 2 FASTQsim LongISLND For an exhaustive list of ...
user avatar
9 votes
Accepted

Extract nanopore read ID & start times from fastq file

awk '{if(NR%4==1) print $1, $5}' file.fastq | sed -e "s/ start_time=/, /" -e "s/^@//" The awk command gets the first of every ...
user avatar
  • 19.3k
9 votes

Tools for simulating Oxford Nanopore reads

By chance, just today I've heard of a nanopore read simulator, NanoSim. It is released under a GPL license. I have never used it, though...
user avatar
8 votes
Accepted

Building STAR Genome Index for nanopore RNA sequencing

The parameter is used to determine how much sequence STAR indexes on each side of a splice junction to improve its alignment accuracy. For very long reads, this may not be ideal. I am not sure if ...
user avatar
  • 727
8 votes
Accepted

Total reads aligning to each reference within a bam file

The quick way to get the number of alignments on each reference is samtools idxstats my_bam.bam Number of reads on each reference is column 3. Although, as has ...
user avatar
  • 3,201
8 votes
Accepted

Why do I get so many insertions from Minimap2 on my Nanopore WGS?

Insertions and deletions are the dominant error mode of long read sequencing, including nanopore sequencing. What you see is not unexpected. Things may have improved by now if you would download the ...
user avatar
7 votes

Tools for simulating Oxford Nanopore reads

In addition to the already mentioned NanoSim, there is also SiLiCO and ReadSim (although it hasn't been updated in over 2 years, so I am not sure how relevant it is at this point considering how fast ...
user avatar
  • 2,099
7 votes

Read length distribution from FASTA file

Using Biopython and matplotlib would seem like the way to go, indeed. It really just boils down to three lines of code to get that graph: ...
user avatar
  • 179
7 votes

What are the pros and cons of the different basecallers in Oxford Nanopore Technology Sequencing?

There are also third party free and open source basecallers that haven't been developed by Oxford Nanopore. Of particular note is Chiron, which gave the best uncorrected assembly identity among the ...
user avatar
  • 11.5k
6 votes
Accepted

Compare alignment quality of multiple sequencing runs aligned against the same reference genome

Qualimap will do this for you. Go to qualimap.bioinfo.cipf.es Run qualimap (default params are fine) on each BAM file Open up the HTML output, and you can read off the %identity (they measure the ...
user avatar
  • 952
6 votes
Accepted

How can I improve a long-read assembly with a repetitive genome?

You can't resolve 20kb near identical repeats/segdups with 10kb reads. All you can do is to bet your luck on a few excessively long reads spanning some units by chance. For divergent copies, it is ...
user avatar
  • 5,645
6 votes

Extract nanopore read ID & start times from fastq file

Since the string start_time will only appear on the header line, or else you don't have a valid fastq file, you can simply do: ...
user avatar
  • 7,957
6 votes
Accepted

How can I use Nanopore reads to close gaps or resolve repeats in a short-read assembly?

You might want to look into Unicycler (manuscript with more information can be found here); even though it is supposed to be used with bacterial genomes only, it might work well with a small genome ...
user avatar
6 votes
Accepted

How to convert fastq to fast5

NOTICE: I have altered my answer slightly from the original as I have turned the original script into a pip installable program (with tests) and have updated the ...
user avatar
6 votes
Accepted

Can I stop my nanopore sequencing run if there are no more reads being produced?

Yes, you can click "stop acquisition" and your run won't be negatively affected. All of the reads are saved as they are generated. I am not sure how this will impact live basecalling though if that is ...
user avatar
  • 3,061
6 votes

Significance and timing of "mux scans"

Yes, your understanding is largely correct. This originates from the situation that for each detector on a nanopore array there are 4 pores. I'll explain mux scans and groups, but this is outdated ...
user avatar
5 votes

Visualisation of long read RNA-Seq splicing

DNASTAR's software is for purchase, but high quality. GenVision Pro does genomic visualization, including Sashimi plots. Edit: not sure why this answer is being downvoted, unless it's because the ...
user avatar
5 votes

How do you generate read-length vs read-quality plot for long-read sequencing data (e.g., MinION)?

I also wrote a package to create various plots from Oxford Nanopore sequencing data and alignments: NanoPlot. It can be installed through pip (see also the README on Github). In addition to multiple ...
user avatar
5 votes
Accepted

Detecting structural variants with MinION data

There was a Structural Variant breakout session at the London Calling conference this year. Unfortunately I didn't attend that session, but MinION community members have access to Constance Donnell's ...
user avatar
  • 11.5k
5 votes

Read length distribution from FASTA file

There are several potential approaches. For example: histogram of sequence lengths in the Biopython tutorial plot_distribution from the Ruby-based biopieces framework various solutions to get ...
user avatar
  • 646
5 votes

Read length distribution from FASTA file

You specifically asked about FASTA files, but it's important to always consider read length and quality jointly when assessing high-error long-read data. FASTA files do not provide the quality. This ...
user avatar
  • 1,224
5 votes
Accepted

Split FASTQ and matching BAM into matching chunks

Hmm, it's hard to think of a super efficient way of doing this (assuming the files aren't ordered the same - if they are then this whole answer is basically redundant). And also assuming the read ids ...
user avatar
5 votes
Accepted

STAR-long parameters for aligning RNA ONT reads to genome

I've had great results using minimap2, particularly when combined with a pre-treatment of Canu for error correction (using minimap2 for the read-to-read mapping): ...
user avatar
  • 11.5k
5 votes
Accepted

What are the pros and cons of the different basecallers in Oxford Nanopore Technology Sequencing?

First of all - yes, you can generate FAST5 files and basecall later. Basecalling during the sequencing run is useful if you want results more quickly. You can also recall your FAST5 files with ...
user avatar
  • 525
5 votes

What are the pros and cons of the different basecallers in Oxford Nanopore Technology Sequencing?

It's worth noting two things as of Dec 2018: Albacore is being deprecated (but is still available from the Nanopore developer portal). Guppy is under active development, so Ryan Wick's comparisons ...
user avatar
5 votes
Accepted

How to simulate nanopore reads?

It is important to train an error model as NanoSim does, as we do not fully understand the error processes involved in both the nanopore sequencing process and the basecalling process. Any sort of ...
user avatar
  • 3,061
5 votes
Accepted

Albacore basecalling running but outputs 0 reads

I believe you have multiread fast5 files, as generated by recent versions of MinKNOW. A conversion script is available to convert these to the older, one-read one-file format. AFAIK Albacore is being ...
user avatar
4 votes

Read length distribution from FASTA file

bioawk could be reasonably efficient for this kind of task. ...
user avatar
  • 2,930

Only top scored, non community-wiki answers of a minimum length are eligible