Jit
Enthusiast computational biologist with business dream !!!
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ART: Set of Simulation Tools
By Jit 3549 days agowww.niehs.nih.gov - ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 3417 days agoStructural variation caller tools using long readsBBTools for bioinformatician !
By Surabhi Chaudhary 3080 days ago Comments (1)BBTools can do almost everything now !COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 3151 days agoftp.genomics.org.cn - An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE...TAREAN: A computational tool for identification and characterization of satellite DNA from...
By Surabhi Chaudhary 2991 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...LoRMA: A tool for correcting sequencing errors in long reads
By Abhimanyu Singh 2877 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...SATSUMA : Highly sensitive whole-genome synteny alignments.
By Jit 3723 days agosatsuma.sourceforge.net - Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps only the parts that are orthologous, i.e. following the conserved order and orientation of features, such as protein coding genes,...GenomeComp
By Jit 3443 days agowww.mgc.ac.cn - GenomeComp is a tool for summarizing, parsing and visualizing the genome wide sequence comparison results derived from voluminous BLAST textual output, so as to locate the rearrangements, insertions or deletions of genome segments between species or...rHAT: a seed-and-extension-based noisy long read alignment tool
By Abhimanyu Singh 2860 days agogithub.com - rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT)...Mulan: MUltiple sequence Local AligNment and conservation visualization tool
By Rahul Nayak 3290 days agomulan.dcode.org - Mulan performs multiple (2 or more) sequence alignments with an efficient and rapid "full local" alignment strategy that ensures a recapitulation of evolutionary sequence rearrangements (such as inversions and reshuffling) in any of the species. It...
