phyloFlash
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HRGV
phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
I am hoping to run Phyloflash with a different database than SILVA - specifically the PR2 database instead. I am wondering if this has been done/is possible? If so please...
Hello! I am wondering if there is an option to recover only partially assembled rRNAs sequences? This is the command line I'm using at the moment: phyloFlash.pl -lib 16S_${i} -read1...
Hi there, General question, but is it possible to run phyloflash with multiple datasets at a time? Hoping to compare marine microbial communities at different depths/times so have to run...
hi; so sorry to bother you my code is: phyloFlash.pl -lib phyloFlash_db -almosteverything -read1 ST2019_10_8_FDME220033526-1r_HNJLMDSX2_L2_clean_1.fastq -read2 ST2019_10_8_FDME220033526-1r_HNJLMDSX2_L2_clean_2.fastq -readlength 150 and the error is [08:51:18] running subcommand: /home/lishuxian/anaconda3/envs/pf/bin/bbmap.sh fast=t minidentity=0.7 -Xmx20g...
Hi, I have a weird issue, for two of my samples a number of files are not generated. The _bbmap.sam_ file and _histogram_ are made, but then the rest is...
Hey, thanks a lot for building such an amazing tool with great documentation. I was using the tool using the following command and it seems to fail while running Emirge....
Hi and thanks for creating this tool. It appears to be exactly what I am looking for! I am however having problems creating the database. I am using phyloFlash v3.4...
Hi, I'm running phyloFlash v3.3b2 with default parameters, with the exception of -readlength. I noticed that the SSU rRNA assembly-based taxa output in the summary shows an E-value of -1....
tag was causing single read mode to break, removing it make the pipeline run smoothly.
Hi there, I'm trying to run phyloflash on a MacOS and having an issue while trying to create the initial database. It gets through to the bowtie build step and...