-
I just wanted to mention that I've observed a few times, only when nanopore data is included, that guessed X coverage is estimated to be 4-6x higher than it should be.
I am curious about what effect…
-
I find if I do this:
$bin/tgStoreDump -contigs -bubbles -sizes -s $G -G $GKP -T $TGS 1
It gives larger size stats (i.e. NG50) than what I get size stats from the lengths of sequences in contigs.fasta…
-
I'm attempting to correct a large number of pacbio reads (~ 160Gbase) with unitigs from CA and about 70X illumina (~ 1B 150bp PE reads).
I split the pacbio reads into 8585 chunks as suggested in your …
-
First of all, thanks for helping to choose the parameters. We finished 2nd run on 27X coverage 3G genome. We had
lenContig ng50 393884 bp lg50 1780 sum 1500229865 bp
So it reached 400kb …
-
Some initial kmer are not present in the unitigs
-
Hello,
I could run canu successfully, and canu generated '.contigs.fasta' which consists of many contigs.
I found that some contigs are (not fully but highly) overlapping each other.
Originally, I exp…
-
I am assembling a genome with high heterozygosity. After running Canu using the default parameters, I got many reads that are in the categories of `span-repeat`, `uniq-repeat-cont`, `uniq-repeat-dove`…
-
I recently was running the abyss-map step with the same input file (and same reference unitigs) on different machines to see if one runs this part faster then the other. As a consequence I was able to…
-
Hi,
I am using canu on two different PacBio ccs datasets. One is assembled without issues, but the second terminates at Unitiging stage. Both unitiging attempts failed. Removing 4-unitigger/ and re-ru…
-
Thanks for solving my last issue. Now I ran into a second one.
I am starting canu with
`nice -15 canu -p asm -d 00-assembly genomeSize=0.45g -pacbio-corrected ../../../data/pacBio/02_proovread_correc…