2234 days ago
minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining, and SIMD-parallel Smith-Waterman-Gotoh extension.2233 days ago
WhatsHap: fast and accurate read-based phasing
WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly...nbsp;WhatsHap: fast and accurate read-based phasing) Works well with Ill...requirements (Garg et al., Read-Based P...2229 days ago
mScaffolder: A comparative genome scaffolding tool
A comparative genome scaffolding tool based on MUMmer mScaffolder scaffolds a genome using an existing high quality genome as the reference. It aligns the two genomes usin...2211 days ago
SWALO: Scaffolding with assembly likelihood optimization
SWALO (scaffolding with assembly likelihood optimization) is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing. Please email your questions, comments, suggestions, and bug reports to atif.bd@gmail.com.2206 days ago
AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data AfterQC can simply go through al...p and can be found at: https://github.com/OpenGene/fastp . If you prefer a C++ based t...2197 days ago
2193 days ago
RNA-seq Analysis Workshop Course Materials
RNAseq can be roughly divided into two "types": Reference genome-based - an assembled genome exists for a species for which an RNAseq experi...ult to do well. In this lesson we will focus on the Reference genome-based t...2193 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts. The fo...ers within specified coverage and GC tolerances. seq: Filters a sequence file based o...2042 days ago
ReMILO: reference assisted misassembly detection algorithm using short and long reads.
ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the co...2190 days ago