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.2188 days ago
pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., ....2188 days ago
GenomeMapper: Simultaneous alignment of short reads against multiple genomes
GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to alig...2187 days ago
2184 days ago
WhatsHap: fast and accurate read-based phasing
...phasing genomic variants using DNA sequencing reads, also called read-based phasi...e assembly. It is especially suitable for long reads, but works also well with sho...na, PacBio, Oxford Nanopore and other types of reads It phases SNVs, indels and e...2184 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
...cbio.fq.gz > aln.sam # PacBio genomic reads ./minimap2 -ax map-ont ref.f...> aln.sam # Oxford Nanopore genomic reads ./minimap2 -ax sr ref.fa rea...# PacBio read overlap ./minimap2 -x ava-ont reads.fa reads.fa > overlaps.paf...2161 days ago
AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
...data AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC results of each fa...2152 days ago
2148 days ago
RNA-seq Analysis Workshop Course Materials
...ts for a species for which an RNAseq experiment is performed. It allows reads to be aligned against the ref...s of interest is available. In this case one would need to assemble the reads into transcripts using de nov...2148 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
...quence in a file using K-mers from another sequence file. blob: Given, reads and an assembly, calculates b...ally this is used to compare two K-mer hashes produced by different NGS reads. profile: Creates a K-mer co...1997 days ago