AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only require...2094 days ago
Snippy: Rapid haploid variant calling and core SNP phylogeny
...s a consistent set of output files in a single folder. It can then take a set of Snippy results using the same reference and generate a core SNP alignment (and ultimately a phylogenomi...2020 days ago
2086 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
...combine both technologies and the more erroneous long reads are corrected using the short reads. Current approaches rely on various graph based alignment techniques and do not take th...2080 days ago
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
Mulan: Multiple-sequence local alignment and visualization for studying function and...anscription factor binding sites in multiple alignments. In addition, Mulan supports...wo-way communication with the GALA database; alignments of multiple species dynamica...2076 days ago
LoRMA: A tool for correcting sequencing errors in long reads
...s only. The method consists of two phases: first, we use an iterative alignment-free correction method based...lished using long-distance dependencies that are found using multiple alignments. According to our experiment...2063 days ago
LSC: Improving PacBio Long Read Accuracy by Short Read Alignment
Added Command line argument support. Multi-stage execution modes. Support for parallelization. Now execution proceeds in batches of long reads the size of which can...2063 days ago
Qualimap2: Evaluating next generation sequencing alignment data
...ation written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its deriv...2059 days ago
Rebaler: program for conducting reference-based assemblies using long reads.
Rebaler is a program for conducting reference-based assemblies using long reads. It relies mainly on minimap2 for alignment and Racon for making consensus sequences...2051 days ago
KAST: Perform Alignment-free k-tuple frequency comparisons from sequences
Perform Alignment-free k-tuple frequency comparisons from sequences. This can be in the form of two input files (e.g. a reference and a query) or a single file for pairwise comparisons to be made.2049 days ago