Rahul Nayak
A Bioinformatician
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The "Ifs" and "Buts" of NGS Quality Control and Trimming
By BioStar 429 days agoNGS quality control and trimming are essential steps to ensure reliable and accurate data for analysis. While the "ifs" highlight the clear benefits of these steps, the "buts" remind us of the potential pitfalls. By adopting best practices and...HipSTR: Haplotype inference and phasing for Short Tandem Repeats
By BioJoker 2557 days agogithub.com - HipSTR was specifically developed to deal with these errors in the hopes of obtaining more robust STR genotypes. In particular, it accomplishes this by: Learning locus-specific PCR stutter models using an EM algorithm Mining candidate...ONT assembly and Illumina polishing pipeline
By Jit 3026 days agogithub.com - This pipeline performs the following steps: Assembly of nanopore reads using Canu. Polish canu contigs using racon (optional). Map a paired-end Illumina dataset onto the contigs obtained in the previous steps...dnaPipeTE: de-novo assembly & annotation Pipeline for Transposable Elements
By Rahul Nayak 3017 days agogithub.com - dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs...Ra assembler - a de novo DNA assembler for third generation sequencing data
By biogeek 2992 days agogithub.com - Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS). Ra is in...AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
By Manisha Mishra 2881 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...ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
By Rahul Nayak 2805 days agofaculty.cse.tamu.edu - With increased availability of de novo assembly algorithms, it is feasible to study entire transcriptomes of non-model organisms. While algorithms are available that are specifically designed for performing transcriptome assembly from...QUAST-LG: Versatile genome assembly evaluation
By Jit 2690 days agocab.spbu.ru - QUAST-LG-a tool that compares large genomic de novo assemblies against reference sequences and computes relevant quality metrics. Since genomes generally cannot be reconstructed completely due to complex repeat patterns and low coverage regions, we...MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via...
By Jit 2671 days agogithub.com - MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to...CANU genome assembly parameters !
By Rahul Nayak 2616 days agoChoose the appropriate parameters to run Canu and run it.
