Jit
Enthusiast computational biologist with business dream !!!
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SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins
By BioStar 825 days agogithub.com - SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes...Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator
By Jit 3425 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 2872 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 3217 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 2891 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 1465 days agoBooks and research paper to readLRCstats: a tool for evaluating long reads correction methods
By Aaryan Lokwani 2970 days agogithub.com - LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted by third generation sequencing technology such as machines produced by Pacific Biosciences. The reads produced by third generation...BASE: a practical de novo assembler for large genomes using long NGS reads
By Rahul Nayak 2912 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...Genome assembly tutorial "Genome Assembly for short and long reads"
By Jit 2820 days ago Comments (1)bioinformaticsdotca.github.io - In this lab we will perform de novo genome assembly of a bacterial genome. You will be guided through the genome assembly starting with data quality control, through to building contigs and analysis of the results. At the end of the lab you will...PBSuite: Software for Long-Read Sequencing Data from PacBio
By Jit 3511 days agosourceforge.net - PBJelly - the genome upgrading tool. PBHoney - the structural variation discovery tool Both are contained within the PBSuite code found in downloads.----- PBJelly -----Read The...
