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.
Hi @kbseah , is there a way for me to find out the alignment identity between individual reads and their closest database hit from the output files? Thanks! Josephine
Hi there, Firstly, I would like to really appreciate the development of the tool, it has been helping me a lot !! Recently, while running phyloflash I am getting the...
Hello! Thank you for the tool. I have shotgun data from single isolates and assembled genomes (SPAdes for isolates). My goal was to extract rRNA from assembled genomes, but now...
Hey, I'm using `phyloFlash_compare.pl` to visualize the data generated using PhyloFlash. The script is able to generate barplot,matrix, and ntu_table but errors out when creating the heatmap. Do you think...
Hello, I am trying to install PhyloFlash but when I check for dependencies with: `phyloFlash.pl -check_env` I get this message: `Unable to find all required tools. These are missing: [11:48:47]...
Hi, Im trying to run the phyloFlash.pl script on single-read Data basepair length 75. The provided testcase to check if installation was successful is running without issuses. -env test approves...
Dear Creators, I ran twice phyloflash with different data bases; one with PR2 and used the `-readlimit` to only used the first 3000000 reads, the line of code I used...
Build database automatically with LTP sequences (https://www.arb-silva.de/projects/living-tree/) instead of SILVA NR Ref database. Motivation is to have a smaller database with authoritative classifications, more suitable for taxonomic classification, cf: https://www.drive5.com/usearch/manual/faq_tax_db.html...
User suggestion: Add option to only perform read filtering and report mapped reads, and not continue further with taxonomic summary and assembly.
Additional packages that are needed for the R-script are installed after all data is already read in. If this fails, the execution is halted, but the script still reports the...
