Abhimanyu Singh
A bioinformatics beginner
Our Sponsors
Related items
Pacbio Long Reads Compatible Software and Tools
By Archana Malhotra 3279 days agogithub.com - The following software packages are known to be compatible with PacBio® data, in addition to PacBio's own SMRT® Analysis suite. All packages are believed to be open source or freely available for non-commercial use. See the individual...Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator
By Jit 3209 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,...NanoSim: nanopore sequence read simulator based on statistical characterization.
By Jit 3001 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...ChIPulate: A Python3 framework to simulate read counts in a ChIP-seq experiment
By Abhimanyu Singh 2539 days agogithub.com - ChIP-seq simulation pipeline, ChIPulate, we assess the impact of various biological and experimental sources of variation on several outcomes of a ChIP-seq experiment, viz., the recoverability of the TF binding motif, accuracy of TF-DNA binding...Meraculous: De Novo Genome Assembly with Short Paired-End Reads
By Jit 3042 days agowww.ncbi.nlm.nih.gov - We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia...TAREAN: A computational tool for identification and characterization of satellite DNA from...
By Surabhi Chaudhary 2853 days agobitbucket.org - TAndem REpeat ANalyzer -TAREAN – is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their...
Short-read assembly using Spades !
Last updated 1496 days ago by Abhimanyu Singh Comments (2)If we only had Illumina reads, we could also assemble these using the tool Spades. You can try this here, or try it later on your own data. Get data We will use the same Illumina data as we used above: illumina_R1.fastq.gz: the Illumina...GAEMR
By Jit 3553 days agowww.broadinstitute.org - The Genome Assembly Evaluation Metrics and Reporting (GAEMR) package is an assembly analysis framework composed a number of integrated modules. These modules can be executed as a single program to generate a complete...mrFAST: Micro Read Fast Alignment Search Tool
By Neel 3602 days agomrfast.sourceforge.net - mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold,...mafTools
By Radha Agarkar 3576 days agogithub.com - Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.
