metAMOS
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marbl
A metagenomic and isolate assembly and analysis pipeline built with AMOS
Future versions of metAMOS/iMetAMOS should include assembly polishing/improvement tools such as Pilon (http://www.broadinstitute.org/software/pilon/) or iCORN (http://icorn.sourceforge.net/).
Currently, the MapReads report only includes the contig coverage histogram. Include % reads mapped to contigs and % reads mapped between multiple contigs and maybe link histogram
Propagate support metaphyler and PhyloSift but not BLAST or phmmer or PhymBL. Add support for propagating their classifications
When newbler runs, it can split a read within assembly into multiple pieces. Currently metAMOS will only take the first occurrence of the read.
Hi, It is unclear to me based on the documentation how the Blast-ing works. I did not download the DB with the package. However, I do have myriad blast databases...
I have been working on getting metAMOS 1.3 installed on a linux server on our super computer. I am running into many problems getting this up and running due to...
Hi everyone, I am trialling MetAMOS on metagenomics data and getting some errors at the FindRepeats step. I first performed a trial run with a sample of the my fastq...
Currently, toAmos_new can fail silently and the pipeline keeps going. If a bank is missing, subsequent steps will fail and so the pipeline needs to abort. Example failure: metaAMOS/treangen-metAMOS-37e78da/AMOS/Linux-x86_64/bin/toAmos_new: error...