Abhimanyu Singh
A bioinformatics beginner
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Magic-BLAST: a tool for mapping large next-generation RNA or DNA sequencing runs against a whole...
By Jit 2524 days agoncbi.github.io - Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of...Hawkeye: an interactive visual analytics tool for genome assemblies
By Abhimanyu Singh 2153 days agoamos.sourceforge.net - Genome sequencing remains an inexact science, and genome sequences can contain significant errors if they are not carefully examined. Hawkeye is our new visual analytics tool for genome assemblies, designed to aid in identifying and correcting...GMOL: An Interactive Tool for 3D Genome Structure Visualization
By Jit 2440 days agowww.nature.com - GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve...SALSA: A tool to scaffold long read assemblies with Hi-C
By Jit 2354 days agogithub.com - This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch. To use the latest version,...vt: a variant tool set that discovers short variants from Next Generation Sequencing data.
By Jit 1762 days agogenome.sph.umich.edu - vt is a variant tool set that discovers short variants from Next Generation Sequencing data. https://genome.sph.umich.edu/wiki/Vt https://github.com/atks/vtLoRMA: A tool for correcting sequencing errors in long reads
By Abhimanyu Singh 2270 days agogite.lirmm.fr - An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are...iSeqQC: a tool for expression-based quality control in RNA sequencing
By BioStar 1743 days agogithub.com - iSeqQC, an expression-based QC tool that detects outliers either produced due to variable laboratory conditions or due to dissimilarity within a phenotypic group. iSeqQC implements various statistical approaches including unsupervised clustering,...Ra assembler - a de novo DNA assembler for third generation sequencing data
By biogeek 2523 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 2412 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...Converting a VCF into a FASTA given some reference !
By Jit 2319 days agoconverting a VCF file into a FASTA file given a reference sequence
