Rahul Nayak
A Bioinformatician
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HaploTypo: a variant-calling pipeline for phased genomes
By Jit 1802 days agogithub.com - An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, most genetic variant calling tools do not explicitly account for haplotype structure. Here, we present HaploTypo, a pipeline tailored to resolve...PyParanoid: a pipeline for rapid identification of homologous gene families in a set of genomes
By BioStar 1564 days agogithub.com - PyParanoid is a pipeline for rapid identification of homologous gene families in a set of genomes - a central task of any comparative genomics analysis. The "gold standard" for identifying homologs is to use reciprocal best hits (RBHs) which depends...JCVI utility libraries
By Jit 1296 days agogithub.com - Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.pipesnake: bioinformatics best-practice analysis pipeline for phylogenomic reconstruction
By LEGE 277 days agogithub.com - ausarg/pipesnake is a bioinformatics best-practice analysis pipeline for phylogenomic reconstruction starting from short-read 'second-generation' sequencing data. The pipeline is built using Nextflow, a workflow tool to run tasks across...shovill: Assemble bacterial isolate genomes from Illumina paired-end reads
By BioStar 1422 days agogithub.com - Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take...ARCS: scaffolding genome drafts with linked reads
By Rahul Nayak 2455 days agogithub.com - ARCS, an application that utilizes the barcoding information contained in linked reads to further organize draft genomes into highly contiguous assemblies. We show how the contiguity of an ABySS H.sapiensgenome assembly can be increased over...MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
By Rahul Nayak 2389 days agogithub.com - MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorithms that are much more efficient than the state of art of aligners and...Jvarkit : Java utilities for Bioinformatics
By Jit 2361 days agolindenb.github.io - Collection of Java tool kits for bioinformatics works: Jvarkit : Java utilities for BioinformaticsnpScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads
By Shruti Paniwala 2358 days agojapsa.readthedocs.io - npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbial datasets. In real-time mode, it can be integrated with simple...SimLoRD: A read simulator for third generation sequencing reads
By Aaryan Lokwani 2286 days agobitbucket.org - SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model. Reads are simulated from both strands of a provided or randomly generated reference sequence. The reference...
