Jit
Enthusiast computational biologist with business dream !!!
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Hercules: a profile HMM-based hybrid error correction algorithm for long reads
By Jit 2288 days agogithub.com - Choosing whether to use second or third generation sequencing platforms can lead to trade-offs between accuracy and read length. Several studies require long and accurate reads including de novo assembly, fusion and structural variation detection....BASE: a practical de novo assembler for large genomes using long NGS reads
By Rahul Nayak 2229 days agogithub.com - new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE...wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly
By BioStar 2121 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...AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads
By Rahul Nayak 1351 days agogithub.com - AlignGraph2 is the second version of AlignGraph for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome. More...Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator
By Jit 2741 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,...SISRS: Site Identification from Short Read Sequences
By Abhimanyu Singh 2188 days agogithub.com - Next-gen sequence data such as Illumina HiSeq reads. Data must be sorted into folders by taxon (e.g. species or genus). Paired reads in fastq format must be specified by _R1 and _R2 in the (otherwise identical) filenames. Paired and unpaired reads...NanoSim: nanopore sequence read simulator based on statistical characterization.
By Jit 2534 days agowww.bcgsc.ca - NanoSim, a fast and scalable read simulator that captures the technology-specific features of ONT data and allows for adjustments upon improvement of nanopore sequencing technology. The first step of NanoSim is read characterization, which provides...BamView: a free interactive display of read alignments in BAM data files
By Neel 2207 days agobamview.sourceforge.net - To run the application on UNIX from the downloaded jar file run the UNIX: java -mx512m -jar BamView.jar and extra command line options are given when '-h' is used: java -jar BamView.jar -h BAM files can be specified on the command line with the...Must read paper and books in evolution biology !
By Abhi 781 days agoBooks and research paper to readdcGOR
By Martin Jones 3669 days agoan R package for analysing ontologies and protein domain annotations
