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EAGLER: a scaffolding tool for long reads.
By Jit 2832 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...Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
By Rahul Nayak 2695 days agosourceforge.net - Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method. Then, Rainbow implements a heterozygote calling like...Filtlong: quality filtering tool for long reads
By Radha Agarkar 2123 days agogithub.com - Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the...Pacbio Long Reads Compatible Software and Tools
By Archana Malhotra 3278 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...CABOG: Celera Assembler with Best Overlap Graph
By Abhimanyu Singh 3217 days agowww.jcvi.org - CABOG (Celera Assembler with Best Overlap Graph) is scientific software for DNA research. CABOG has been a critical component of many genome sequencing projects. CABOG operates on small genomes such as bacterial as well as large genomes such as...BBTools for bioinformatician !
By Surabhi Chaudhary 2941 days ago Comments (1)BBTools can do almost everything now !QuorUM: An Error Corrector for Illumina Reads
By BioStar 2222 days agowww.genome.umd.edu - We produce trimmed and error-corrected reads that result in assemblies with longer contigs and fewer errors. We compared QuorUM against several published error correctors and found that it is the best performer in most metrics we use. QuorUM is...Common steps for reads mapping !
By BioStar 1093 days agoMapping reads to a reference genome is an essential step in many types of genomic analysis, such as variant calling and gene expression analysis.SOAP2 : Short Oligonucleotide Analysis Package 2
By Poonam Mahapatra 2844 days agosoap.genomics.org.cn - SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment. The new program features in super fast and accurate alignment for huge amounts of...PureCN: copy number calling and SNV classification using targeted short read sequencing
By Jit 2766 days agobioconductor.org - This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with...
