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.
Factor in edge case with custom DB when reference sequences too short to report paired end insert size.
Hello! Currently when running `phyloFlash_makedb.pl` it is built in [current directory](https://github.com/HRGV/phyloFlash/blob/master/phyloFlash_makedb.pl#L279). I think it would be useful to allow users to specify this on the command line similar to how...
User database may contain sequences that are shorter than 800 bp minlength limit hard-coded to the UniVec filtering step in `phyloFlash_makedb.pl`. See issue #115. Allow user to change this option...
In addition to trusted contigs, optionally supply PacBio or Nanopore long reads for assembly step only. This may help in assembly of closely related strains (?).
Hi phyloFlash team, thanks for developing this awesome tool! My question is related to the taxonomy assignment of NTU for Eukaryotic sequences. I know that Eukaryote has much more taxonomic...
Dear phyloflash author, when fasta file were used for spades.py assembly there was an error about not recognizing phred format. Add this line will solve the problem (most current sequncer...
Hello and thanks for the self-contained, all-in-one super tool! I have generated a database using `phyloFlash_makedb.pl` based on 16S sequences extracted from genomes as follows: ``` phyloFlash_makedb.pl \ --silva_file /home/flejzerowicz/softs/phyloflash/wol/SILVA_WOL_DB.fasta...
Bitflag 0x1 not set with SE reads, so no assumptions can be made about 0x40 or 0x80 Need separate subroutine to handle SE reads taxonomy hashing.
With `no-split` option, get error message that 'axis.ticks.margin' is deprecated. Error message below... ``` $ phyloFlash_heatmap.R -v -d -o test01.png --library-name-from-file --no-split ./*.csv Loading required package: optparse Loading libraries Selected...
I'm filing this report for Malin... Heatmap script breaks when only one taxon present in 'Eukaryota'. `hclust` requires at least 2 objects to cluster. Verbose output copied below... ``` $...