Rahul Nayak
A Bioinformatician
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SSPACE
By Jit 3228 days agowww.baseclear.com - SSPACE standard is a stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data. It is unique in offering the possibility to manually control the scaffolding process. By using the distance information of paired-end and/or...Finishing !!
By Jit 3213 days agowww.cbcb.umd.edu - The process of finishing a genome and moving it from a draft stage (the result of sequencing and initial assembly) to a complete genome is typically a time and resource intensive task. The advent of new sequencing technologies...DIYA: a bacterial annotation pipeline for any genomics lab
By Jit 3172 days agosourceforge.net - DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and...MeDuSa: a multi-draft based scaffolder
By Abhimanyu Singh 2943 days agogithub.com - MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained from a set of (draft or closed) genomes from related organisms to determine the correct order and orientation of the contigs. MeDuSa...pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
By Jit 2844 days agogithub.com - pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file...
Convert EnsEMBL GTF to Annotation table (Geneid, GeneSymbol, GeneWiseChrLocation, GeneClass,...
Last updated 2777 days ago by Jitendra NarayanBash Script source: https://gist.github.com/santhilalsubhash/367befcf5216be4b1fd9 Information: This script converts EnsEMBL GTF...
ComparativeGenomics Exercise2
By Neel 2753 days agoCOMPARATIVE MICROBIAL GENOMICS ANALYSIS WORKSHOP @ cbs.dtu.dk Free Bioinformatics workbench https://www.mn.uio.no/ifi/english/research/networks/clsi/earlier_seminars/2012/tammivesth_osloseminarfinal.pdfBASE: a practical de novo assembler for large genomes using long NGS reads
By Rahul Nayak 2696 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...CANU genome assembly parameters !
By Rahul Nayak 2616 days agoChoose the appropriate parameters to run Canu and run it.Introduction to Bioinformatics
By eliabrodsky 2467 days agoLearn about bioinformatics online by watching videos, reading engaging articles and practicing bioinformatics skills using public domain datasets.
