User Activity
-
Posted
a comment
on
discussion General Discussion
on
metassembler
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
-
Posted
a comment
on
discussion General Discussion
on
metassembler
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 [email protected] 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...
-
Posted
a comment
on
discussion General Discussion
on
metassembler
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 <[email protected]> wrote: > Hi, I'm trying to figure out how to use a single, interleaved paired-end > library in metassembler....
-
Posted
a comment
on
discussion General Discussion
on
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 [email protected] wrote: Hi Michael Yes that is what I saw in your paper and it is a species closely related...
-
Posted
a comment
on
discussion General Discussion
on
metassembler
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:...
-
Posted
a comment
on
discussion General Discussion
on
metassembler
Hi Tim, Glad we are making progress. Im guessing what happened is one of your assemblies...
-
Posted
a comment
on
discussion General Discussion
on
metassembler
Hi Tim, I'm not at my desk but I think one is supposed to have contigs and one will...
-
Posted
a comment
on
discussion General Discussion
on
metassembler
It is not well tested, and I would try a very small example first to confirm that...
Personal Data
- Username:
- mcschatz
- Joined:
- 2004-09-15 17:06:11
Projects
This is a list of open source software projects that Michael Schatz is associated with:
- AMOS AMOS is a collection of tools for genome assembly Last Updated:
- Bowtie Last Updated:
- CloudBurst Last Updated:
- Contrail Last Updated:
- FLASH Merge mates from fragments that are shorter than twice the read length Last Updated:
-
Genome Mappability Score Analyzer Last Updated:
- Jnomics Jnomics is a collection of cloud-scale DNA sequence analysis tools Last Updated:
- MUMmer Last Updated:
- MUMmerGPU Last Updated:
- Slice Tools Last Updated:
- SplitMEM Graphical pan-genome analysis with suffix skips Last Updated:
- Whole-Genome Shotgun Assembler Last Updated:
- inVUE Last Updated:
- metassembler Last Updated:
- scalpel Genetic variants discovery tool Last Updated:
