Sequanix: a dynamic graphical interface for Snakemake workflows
...alone applications: sequana_coverage ease the extraction of genomic regions of interest and genome coverage information sequana_taxonomy performs a quick taxonomy of your FastQ. This requires...1594 days ago
PhiSpy: PhiSpy identifies prophages in Bacterial (and probably Archaeal) genomes
...bsp;Edwards Bioinformatics Lab Improvements, bug fixes, and other changes were made by Katelyn McNair Edwards Bioinformatics Lab and Przemyslaw Decewicz DEMB at the...1454 days ago
1336 days ago
DADA2: Fast and accurate sample inference from amplicon data with single-nucleotide resolution
...emoves primers on both ends of each ITS read, a key step due to the variable length of the ITS region. Short demonstrations of assigning taxonomy and assigning speci...1321 days ago
EUKulele: Taxonomic annotation of the unsung eukaryotic microbes
EUKulele, an open-source software tool designed to assign taxonomy to microeukaryotes detected in meta-omic samples, and complement analysis approaches in other domains by accommodating assembly output and providing concrete metrics reporting the taxonomic completeness of each sample.1276 days ago
1257 days ago
CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes
The pipeline can use information from scaffolded assemblies (for example from HiC or 10X Genomics), or even from diverged (~65-100 Mya) reference genomes for ordering the contigs an...1202 days ago
Pandoc: a universal document converter
If you need to convert files from one markup format into another, pandoc is your swiss-army knife. Pandoc can convert almost all formats https://pandoc.org/index.html1096 days ago
k-mers tutorial - classification and taxonomy
...p;computing and searching k-mer-based sketch search databases for all the things. But I haven't spent too much talking about using k-mers for taxonomy, although that has become an&...1033 days ago
VCF2PopTree: a client-side software to construct population phylogeny from genome-wide SNPs
...p; Furthermore, it displays the tree in a mobile phone (iPhone and Android) if the input file size is small. CITATION: Subramanian, S., Ramasamy, U. and Chen, D. (2019). ...912 days ago