Abhimanyu Singh
A bioinformatics beginner
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multiPhATE: bioinformatics pipeline for functional annotation of phage isolates
By Abhimanyu Singh 2017 days agogithub.com - multiple-genome Phage Annotation Toolkit and Evaluator (multiPhATE). multiPhATE is a throughput pipeline driver that invokes an annotation pipeline (PhATE) across a user-specified set of phage genomes. This tool incorporates a de...MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
By Jit 1764 days agogithub.com - MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome...EUKulele: Taxonomic annotation of the unsung eukaryotic microbes
By Shruti Paniwala 1427 days agogithub.com - EUKulele, an open-source software tool designed to assign taxonomy to microeukaryotes detected in meta-omic samples, and complement analysis approaches in other domains by accommodating assembly output and providing concrete metrics reporting...MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
By Neel 1087 days agogithub.com - MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenome assembly together with annotation and visualization results from HTS raw...CLgenomics
By Radha Agarkar 2821 days agochunlab.wordpress.com - CLgenomics is a standalone desktop software specifically designed for bacterial genome analysis. This program has a powerful multi-genome browser, which enables rapid and responsive exploration of bacterial genomes. To use CLgenomics, individual...SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences
By Jit 2172 days agolbbe.univ-lyon1.fr - The software package SiLiX implements an ultra-efficient algorithm for the clustering of homologous sequences, based on single transitive links (single linkage) with alignment coverage constraints. SiLiX adopts a graph-theoretical framework to...Snippy: Rapid haploid variant calling and core SNP phylogeny
By Neel 2295 days agogithub.com - Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is...NCBI PSI-BLAST Tutorial
By Jitendra Narayan 4109 days agohttp:--www.biotechnology.jhu.edu- Tutorial for PSI-BLAST, an extension of BLAST that uses matrix algebra. BLAST is a cornerstone bioinformatics tool at NCBI. BLAST is the Basic Local Alignment Search tool and will protein and DNA sequences that are...A fast package to parse BLAST
By Jitendra Narayan 4091 days ago, managBlaSTorage: a fast package to parsee and store BLAST results
