Jit
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nQuire: a statistical framework for ploidy estimation using next generation sequencing
By Jit 2241 days agogithub.com - nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens, artificial selection experiments, and for historical or ancient samples where...NanoPack: visualizing and processing long-read sequencing data
By Jit 2158 days agogithub.com - The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible...Prof. Dr. med. Andreas Ramming
In many autoimmune diseases, a misdirected immune response leads to chronic inflammation and subsequently to fibrotic and degenerative tissue remodeling. Therapeutic options are available for inflammatory joint diseases, but only about 40% of...FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
By Jit 1760 days agobioinfo.ut.ee - FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the...HASLR: a hybrid assembler which uses both second and third generation sequencing reads
By BioStar 1663 days agogithub.com - HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of...Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1001 days agogithub.com - This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA +...dcGOR
By Martin Jones 3667 days agoan R package for analysing ontologies and protein domain annotationsCANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing.
By Jit 3132 days ago Comments (2)github.com - Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). The software is currently alpha level, feel free to use and report issues encountered. Canu is...
BBMap/BBTools package: Multipurpose tool designed for converting reads or other nucleotide data...
Last updated 2915 days ago by JitReformat is a member of the BBMap/BBTools package. It is a multipurpose tool designed for converting reads or other nucleotide data between different formats. It supports, and can inter-convert: fastq fasta fasta+qual sam scarf (an old Illumina...
