Michael Schatz

Hi Bob, Thanks for the note. Columns 1-8 are the only ones that are needed to assemble the final contigs using meta2fasta.pl. The additional columns are debugging codes and coordinates of the original assemblies encoding the status of the CE statistic over the breakpoints of the alignments. Since they are not used in the downstream analysis, you can safely ignore them. Good luck Mike

There is also a script here that can be used to run the alignments in parallel on an sge-based grid: https://github.com/fritzsedlazeck/sge_mummer It will require a bit of code editing, but can get the job done Good luck Mike On Wed, Aug 30, 2017 at 11:20 AM, Alejandro Hernandez Wences ahwences@users.sf.net wrote: You should try usign different -l and -c paramteres for nucmer (this can be done with the parameters nucmer_l and nucmer_c in the conf file). For large or very repetitive genomes I would...

ERROR! The markdown supplied could not be parsed correctly. Did you forget to surround a code snippet with "~~~~"?Thanks for your interest, but unfortunately interleaved fastq files are not supported. Id recommend you deinterleave the fastq files using a script like this: https://gist.github.com/nathanhaigh/3521724 Good luck! Mike On Mon, May 29, 2017 at 9:22 PM, Charles Bridges <cmb12@users.sf.net> wrote: > Hi, I'm trying to figure out how to use a single, interleaved paired-end > library in metassembler....

Yeah, there must be tons of repeats if it is still stuck in nucmer. As painful as it is, Id kill the job and start again with different nucmer settings. I would recommend: -l 100 -c 500 This will (modestly) reduce sensitivity, but could finish in less than a day. If it takes more than a day, boost up -l 100 to -l 250 and try again Good luck! Mike On Wed, May 17, 2017 at 11:02 AM, Astrid astridboehne@users.sf.net wrote: Hi Michael Yes that is what I saw in your paper and it is a species closely related...

Can you tell what phase of the program is currently running? We successfully merged the fish genome from the Assemblathon 2 data set in ~1 day. Here are the notes on it from the supplemental material: For all Fish assemblies and metassemblies we used the available 2Kb mate-pair libraries: 801KYABXX.2 and 801KYABXX.3 Mapping: bowtie2 --maxins 3000 --minins 1000 --threads 16 CE-statistic: mateAn -A 1500 -B 2600 WGA: nucmer –maxmatch -l 50 -c 300 Merges: asseMerge with default options Runtime Requirements:...

Hi Tim, Glad we are making progress. Im guessing what happened is one of your assemblies...

Hi Tim, I'm not at my desk but I think one is supposed to have contigs and one will...

It is not well tested, and I would try a very small example first to confirm that...