Hapsembler: An Assembler for Highly Polymorphic Genomes
Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types of polymorphism. Hapsembler can be used to assemble reads from a variety of platforms including Illumina and Roche/454. http://compbio.cs.toronto.edu/hapsembler/2227 days ago
2226 days ago
SOAP2 : Short Oligonucleotide Analysis Package 2
SOAPaligner/soap2 is a member of the SOAP (Short Oligonuc...st and accurate alignment for huge amounts of short reads generated by Illumina/Solexa...uire only 2 minutes aligning one million single-end reads onto the human reference geno...2226 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.2225 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., ....2225 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 gappe...2224 days ago
2221 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 phasi...y. It is especially suitable for long reads, but works also well with sho...o, Oxford Nanopore and other types of reads It phases SNVs, indels and e...2221 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
git clone https://github.com/lh3/minimap2...z > aln.sam # PacBio genomic reads ./minimap2 -ax map-ont ref.f...sam # Oxford Nanopore genomic reads ./minimap2 -ax sr ref.fa rea...o read overlap ./minimap2 -x ava-ont reads.fa reads.fa > overlaps.paf...2198 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...and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC results of each fa...2189 days ago