HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
...ool for assembling haplotypes from DNA sequence reads, designed to "just work" wit...e assembly methods are specialized for specific read technologies or protocols, wi...ies, including but not limited to: NGS short reads (Illumina HiSeq) clone-base...2196 days ago
TULIP - The Uncorrected Long read Integration Pipeline
...intended as prototypes, and additional components and/or implementations are likely to follow. Tulipseed takes as input alignments files of long reads to sparse short seeds, and o...2196 days ago
2188 days ago
SOAP2 : Short Oligonucleotide Analysis Package 2
...features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa...nitude faster. It require only 2 minutes aligning one million single-end reads onto the human reference gen...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 align against multiple genomes simulanteousl...2186 days ago
WhatsHap: fast and accurate read-based phasing
...ic variants using DNA sequencing reads, also called read-based phasing or haplotype as..., but works also well with short reads. Features Very accur...ford Nanopore and other types of reads It phases SNVs, indels and...t output that is compatible with ReadBackedPhasing Open Source (MI...2183 days ago
SALSA: A tool to scaffold long read assemblies with Hi-C
...on which describes the methods used for scaffolding. Ghurye, J., Pop, M., Koren, S., Bickhart, D., & Chin, C. S. (2017). Scaffolding of long read assemblies using long range c...2165 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
...acbio.fq.gz > aln.sam # PacBio genomic reads ./minimap2 -ax map-ont ref....> aln.sam # Oxford Nanopore genomic reads ./minimap2 -ax sr ref.fa re...eads.fa reads.fa > overlaps.paf # PacBio read overlap ./minimap2 -x ava-on...2160 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
...sands of tracks. Very light server resource requirements. In fact, JBrowse has no back-end server code, just tools for formatting data files to be read directly over HTTP. Serve hug...2151 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
...a file using K-mers from another sequence file. blob: Given, reads and an assembly, calculates both the read and assembly K-mer coverage a...is used to compare two K-mer hashes produced by different NGS reads. profile: Creates a K-mer c...1996 days ago