Next Generation Sequencing (NGS)
https://en.wikipedia.org/wiki/Sequencing
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Rosenberg lab
Research. Research in the lab focuses on mathematical, statistical, and computational problems in evolutionary biology and human genetics. Long-term interests of the lab include topics such as: Human genetic variation Inference of human...
SDA: Long-read sequence and assembly of segmental duplications
By Jit 2138 days agowww.nature.com - Segmental Duplication Assembler (SDA; https://github.com/mvollger/SDA) constructs graphs in which paralogous sequence variants define the nodes and long-read sequences provide attraction and repulsion edges, enabling the partition and assembly of...Miropeats: discovers regions of sequence similarity amongst any set of DNA sequences
By Poonam Mahapatra 1964 days agowww.littlest.co.uk - Miropeats discovers regions of sequence similarity amongst any set of DNA sequences and then presents this similarity information graphically. Sequence similarity searching is a very general tool that forms the basis of many different biological...RePS: Repeat-masked Phrap with scaffolding, a WGS sequence assembler
By Jit 1833 days agoftp.genomics.org.cn - RePS (Repeat-masked Phrap with scaffolding), a WGS sequence assembler, that explicitly identifies exact kmer repeats from the shotgun data and removes them prior to the assembly. The established software Phrap is used to compute meaningful error...LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
By BioStar 1788 days agocsb5.github.io - LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or...MMseqs2: ultra fast and sensitive sequence search and clustering suite
By Abhi 1192 days agogithub.com - MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin)...Seal: SEquence ALignment evaluation suite
By Jit 2564 days agocompbio.case.edu - Seal is a comprehensive sequencing simulation and alignment tool evaluation suite. This software (implemented in Java) provides several utilities that can be used to evaluate alignment algorithms, including: Reading a pre-existing reference...Latest paper on comparison of mapping tools
By Rahul Agarwal 4147 days ago Comments (1)www.biomedcentral.com - A. Hatem, D. Bozdag, A. E. Toland, U. V. Catalyurek "Benchmarking short sequence mapping tools" BMC Bioinformatics, 14(1):184, 2013. http://bmi.osu.edu/hpc/software/benchmark/ http://bmi.osu.edu/hpc/software/pmap/pmap.html Other similiar...Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search
By Jit 1809 days agogithub.com - Reference free SNP search for comparative population genomics: multiple samples run simultanously. **experimental phase, compiles and runs with OpenMPI-1.8.8 with Intel Compiler only Cycles enumeration (aka Bubbles) as part of de novo de bruijn...Snakemake workflow: dna-seq-gatk-variant-calling
By Jit 1996 days agogithub.com - This Snakemake pipeline implements the GATK best-practices workflow for calling small genomic variants.
