Next Generation Sequencing (NGS)
https://en.wikipedia.org/wiki/Sequencing
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Wtdbg2: a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore
By Neel 2256 days agogithub.com - Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2...HASLR: a hybrid assembler which uses both second and third generation sequencing reads
By BioStar 1694 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...Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
By Jit 2580 days agoschatzlab.cshl.edu - Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used...Is reference genome necessary for gene expression study in transcriptome sequencing or for variant...
Started by Rahul Agarwal 4176 days agoLike in case of plant genomes where nature of genome is too complex and huge in size to accomplish complete de novo assembly by current sequencing technology. What would be alternate solution? Can we live in reference free world?
Genome Browsers
Last updated 4146 days ago by Rahul Agarwal Comments (2)Genome Browser is the platform/database used for searching and retreiving sequences and annotation of genomes belong to various eukaryotes, prokaryotes, etc. Following are the weblink for different available...Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator
By Jit 2769 days agosourceforge.net - Grinder is a versatile program to create random shotgun and amplicon sequence libraries based on DNA, RNA or proteic reference sequences provided in a FASTA file. Grinder can produce genomic, metagenomic, transcriptomic, metatranscriptomic,...Platanus
By Jit 3145 days ago Comments (1)platanus.bio.titech.ac.jp - Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data. The latest version is 1.2.4. To cite Platanus, please use the...NextDenovo: string graph-based de novo assembler for TGS long reads
By Jit 1813 days agogithub.com - NextDenovo is a string graph-based de novo assembler for TGS long reads. It uses a "correct-then-assemble" strategy similar to canu, but requires significantly less computing resources and storages. After assembly, the per-base error rate...RNA-Bloom: a fast and memory-efficient de novo transcript sequence assembler
By LEGE 1628 days agogithub.com - RNA-Bloom is a fast and memory-efficient de novo transcript sequence assembler. It is designed for the following sequencing data types: single-end/paired-end bulk RNA-seq (strand-specific/agnostic) paired-end single-cell RNA-seq...MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
By Rahul Nayak 2417 days agogithub.com - MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorithms that are much more efficient than the state of art of aligners and...
