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 o...2157 days ago
Snippy: Rapid haploid variant calling and core SNP phylogeny
Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use as many...2084 days ago
2150 days ago
SimLoRD: A read simulator for third generation sequencing reads
SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Bioscienc...l chromosomes, whose structure is respected when drawing reads. (Simulation of genome...2142 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 evolution Mulan (http://mulan...es identified with Mulan/multiTF can be integrated and overlaid with extensive genome...2140 days ago
P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
P_RNA_scaffolder is a novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragments. The method is suitable for most genomes. The program could utilize Illumina Paired-end RNA-s...instance, PEP_scaffolder ) for scaffolding genome...2126 days ago
Ensembl Variation - Calculated variant consequences
For each variant that is mapped to the reference genome, we identify all overlapping Ensembl transcripts. We then use a rule-based approach to predict the effects that each allel...2124 days ago
SeqMonk:A tool to visualise and analyse high throughput mapped sequence data
...analysis Visualisation of mapped regions against an annotated genome. Flexible quantitation of th...tical analysis of data to find regions of interest Creation of reports containing data and genome annotation...2122 days ago
Qualimap2: Evaluating next generation sequencing alignment data
Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Int...ves like feature counts. Supported types of experiments include: Whole-genome...2122 days ago
funannotate: Eukaryotic Genome Annotation Pipeline
Funannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time...thus funannotate is aimed at simplifying the genome...2114 days ago