Abhimanyu Singh
A bioinformatics beginner
Latest comments
- Jit on Patterns: a modeling tool dedicated to biological network modeling (1956 days ago): https://github.com/fbertran/Patterns
- Abhimanyu Singh on Genome Assembly Tutorial (2906 days ago): This totorial is also very...
- Jit on Next generation sequencing(NGS) books (3766 days ago): Few next generation sequencing resources at...
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Bioinformatics, Genome, NGS, Assembly, Tool, Analysis, Alignment, Genomes, Reads, Read, long, Sequencing, Synteny, Assembler, PacBio, Ancestral, KEGG, Genes, Assemblies, Algorithm, Pipeline, RNA, sequence, annotation, Graph, Books, Lastz, Reference, Mapping, Tutorial, Reconstruction, Format, View, Genomic, Short, Sequences, plot, Gene, Maps, Bacteria, Visual, correction, Variants, Structure, structural, modeling, Method, DISCOVAR, BroadInstitute, SPAdes
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Abhimanyu Singh's bookmarks
YASRA: Reference based assembler
By Abhimanyu Singh 2835 days agogithub.com - YASRA (Yet Another Short Read Assembler) performs comparative assembly of short reads using a reference genome, which can differ substantially from the genome being sequenced. Mapping reads to reference genomes makes use of LASTZ (Harris et al), a...DAGchainer: Computing Chains of Syntenic Genes in Complete Genomes
By Abhimanyu Singh 2846 days agodagchainer.sourceforge.net - The DAGchainer software computes chains of syntenic genes found within complete genome sequences. As input, DAGchainer accepts a list of gene pairs with sequence homology along with their genome coordinates. Using a scoring function which accounts...Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm)
By Abhimanyu Singh 2897 days agohttp://prodigal.ornl.gov/ - Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. Key features of Prodigal...Genome Assembly Tutorial
By Abhimanyu Singh 2906 days ago Comments (1)www.homolog.us - If genomes were completely random sequences in a statistical sense, 'overlap-consensus-layout' method would have been enough to assemble large genomes from Sanger reads. In contrast, real genomes often have long repetitive regions, and they are hard...BIMA V3: an aligner customized for mate pair library sequencing
By Abhimanyu Singh 2911 days agobioinformatics.oxfordjournals.org - Summary: Mate pair library sequencing is an effective and economical method for detecting genomic structural variants and chromosomal abnormalities. Unfortunately, the mapping and alignment of mate pair read pairs to a reference genome is a...CrossMap
By Abhimanyu Singh 3012 days agocrossmap.sourceforge.net - CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10...SPAdes
By Abhimanyu Singh 3151 days ago Comments (1)bioinf.spbau.ru - SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. This manual will help you to install and run SPAdes. SPAdes version 3.7.1 was released under GPLv2 on March 8,...DISCOVAR
By Abhimanyu Singh 3152 days agowww.broadinstitute.org - DISCOVAR is a new variant caller and DISCOVAR de novo a new genome assembler, both designed for state-of-the-art data. Their inputs are chosen to optimize quality while keeping costs low. Currently it takes as input Illumina reads of length 250 or...
