medaka: Sequence correction provided by ONT Research
medaka is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks applied from a pileup...ssembly. It outperforms graph-based methods operating on basecalled data,...1511 days ago
1500 days ago
1479 days ago
The wavefront alignment (WFA) algorithm
The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage ofhomologous regions...d the alignment score s, using O(s^2) memory. Moreover, the WFA exhibits simple data d...1470 days ago
RNA-Bloom: a fast and memory-efficient de novo transcript sequence assembler
RNA-Bloom is a fast and memory-efficient de novo transcript sequence assembler. It is designed for the following sequencing data t...1459 days ago
1445 days ago
SEASTAR: Systematic Evaluation of Alternative STArt site in RNA
SEASTAR (Systematic Evaluation of Alternative STArt site in RNA) is a software package for Transcript...rt Site (TSS) identification and quantification using only RNA-seq data. It assembles novel TSSs based only on RNA-Seq data a...1424 days ago
PyParanoid: a pipeline for rapid identification of homologous gene families in a set of genomes
PyParanoid is a pipeline for rapid identification of homologous gene families in a set...is problematic, as the modern deluge of sequencing data means that comparative genomics analyses could be performed on datase...1424 days ago
proActiv: Estimation of Promoter Activity from RNA-Seq data
proActiv is an R package that estimates promoter activity from RNA-Seq data. proActiv uses aligned reads and genome anno...ribed in Demircioglu et al. Additional data on differential promoters in...n be downloaded here: https://jglab.org/data-a...1424 days ago
SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis
SHAMAN is a shiny application for differential analysis of metagenomic data (16S, 18S, 23S, 28S, ITS and WGS) including bioinformatics treatment of raw reads for targeted metagenomics, sta...1420 days ago