Jean-François Flot

Overlaps counted twice in "Total length (no overlaps)" calculation?

1

I am wondering about how Bandage calculates the "Total length (no overlaps)" statistics. For example here is a toy GFA with only four contigs and two links: H VN:Z:1.0 S...

Trouble understanding the GFAs obtained from wtdbg2

5

I am having trouble understanding the GFAs I obtain using wtdbg2. Here is a simple example as an illustration, using a small bacterial genome. wget https://downloads.pacbcloud.com/public/dataset/MicrobialMultiplexing_48plex/48-plex_sequences/lima.bc1018--bc1018.subreadset.fastq.gz wtdbg2 -x preset2 -i...

using the ElabFTW scheduler as an alternative to e.g. Google Calendar

32

It would be nice to be able to use the ElabFTW scheduler as an alternative to e.g. Google Calendar. This would not require much changes, except adding the possibility to...

Dear Heng, Since minimap2 now estimates per-base sequence divergence, it would be great if there was a way to represent this divergence level with some color in minidot; either as...

Assembling mixtures of PacBio and Nanopore reads

1

Dear Heng, I am trying to assemble a mixture of PacBio and Nanopore reads using minimap2 and miniasm, what would be the best switch for the overlap step? I tried...

save assembled reads in FASTQ format

1

For some very difficult, repeat-full organelle genomes I would like to get the assembled reads in FASTQ format in order to reassemble them using Unicycler. However, at present NOVOplasty only...

weird choice of "best assembly"

3

Here for this assembly although the score does increase with each increase of K the choice made seems particularly poor... Maybe the way the score is calculated is not suited...

It would be great to add options to treat separately soft clips and hard clips - in the case of Nanopore reads, for instance, soft clips can simply be due...

Hi Torsten, I am trying to use your samclip tool to keep all (PacBio HiFi) reads that map on a genome assembly with more than 1000 bp clipped (this is...

It would be great to be able to run tiara directly on fastq files (including gzipped ones) without having to convert them first to fasta. Also, this would allow users...