Jit
Enthusiast computational biologist with business dream !!!
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PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM and Look Ahead...
By Rahul Nayak 3043 days agogithub.com - PERGA - Paired End Reads Guided Assembler PERGA is a novel sequence reads guided de novo assembly approach which adopts greedy-like prediction strategy for assembling reads to contigs and scaffolds. Instead of using single-end reads to construct...PEAR: a fast and accurate Illumina Paired-End reAd mergeR
By Jit 3833 days agowww.exelixis-lab.org - PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. PEAR evaluates all possible paired-end read overlaps and without requiring the...URMAP, an ultra-fast read mapper
By Jit 2166 days ago Comments (1)github.com - URMAP, a new read mapping algorithm. URMAP is an order of magnitude faster than BWA with comparable accuracy on several validation tests. On a Genome in a Bottle (GIAB) variant calling test with 30× coverage 2×150 reads, URMAP achieves...AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
By Manisha Mishra 3092 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...OrthoANI: An improved algorithm and software for calculating average nucleotide identity
By Abhimanyu Singh 2853 days agowww.ezbiocloud.net - OAT uses OrthoANI to measure the overall similarity between two genome sequences. ANI and OrthoANI are comparable algorithms: they share the same species demarcation cut-off at 95~96% and large comparison studies have demonstrated both algorithms to...The wavefront alignment (WFA) algorithm
By BioStar 2289 days agogithub.com - The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage ofhomologous regions between the sequences to accelerate the alignment process. As opposed to traditional dynamic programming algorithms that run in...AGORA: Algorithm for Gene Order Reconstruction in Ancestors
By Jit 1679 days agogithub.com - AGORA stands for “Algorithm for Gene Order Reconstruction in Ancestors” and was developed by Matthieu Muffato in the DYOGEN Laboratory at the École normale supérieure in Paris in 2008. // | | // ) ) // ) )...MEC: Contig Misassembly Correction
By BioStar 2434 days agogithub.com - MEC, to identify and correct misassemblies in contigs. Firstly, MEC takes fragment coverage as the feature to detect the candidate misassemblies. Then, it can distinguish a large number of false positives from the candidate misassemblies based on...QuorUM: An Error Corrector for Illumina Reads
By BioStar 2434 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...You can't install David Brownlee ;-)
By Jit 2713 days agoDon't be silly, you can't install David Brownlee ;-)
