Jit
Enthusiast computational biologist with business dream !!!
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Collection of Graph Visualization tools !
By Neel 1138 days agopangenome.github.io - Standard approaches to genome inference and analysis relate sequences to a single linear reference genome. This is efficient but has a fundamental problem: Differences from this reference are hard to observe and describe in a coherent way. Variation...ShRec3D
By Jitendra Narayan 4090 days agosites.google.com - ShRec3D is a program that aims at reconstructing a genome 3D structure (b) from the sole knowledge of the contacts between different genomic regions (a) as determined by Hi-C (http://www.ncbi.nlm.nih.gov/pubmed/19815776). There are two options to...Illumina reveals first dataset of long reads
By Rahul Agarwal 4579 days agoWith the help of Moleculo technology , acquired by Illumina releases new service for long reads sequencing i.e., FastTrack Long Reads. Average read length is around 8,500 base pairs in release dataset. Best thing about this, there...ONT assembly and Illumina polishing pipeline
By Jit 3026 days agogithub.com - This pipeline performs the following steps: Assembly of nanopore reads using Canu. Polish canu contigs using racon (optional). Map a paired-end Illumina dataset onto the contigs obtained in the previous steps...dnaPipeTE: de-novo assembly & annotation Pipeline for Transposable Elements
By Rahul Nayak 3017 days agogithub.com - dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs...Ra assembler - a de novo DNA assembler for third generation sequencing data
By biogeek 2992 days agogithub.com - Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS). Ra is in...AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
By Manisha Mishra 2881 days agogithub.com - AlignGraph is a software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism. Using AlignGraph AlignGraph --read1 reads_1.fa --read2 reads_2.fa --contig contigs.fa...EAGLER: a scaffolding tool for long reads.
By Jit 2833 days agogithub.com - EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of long reads. The long reads are used to extend the contigs present in the NGS draft and possibly join overlapping...SWALO: Scaffolding with assembly likelihood optimization
By Jit 2818 days agoatifrahman.github.io - SWALO (scaffolding with assembly likelihood optimization) is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing. Please email your questions, comments, suggestions, and bug reports to...Converting a VCF into a FASTA given some reference !
By Jit 2787 days agoconverting a VCF file into a FASTA file given a reference sequence
