Surabhi Chaudhary
A Bioinformatician
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HASLR: a hybrid assembler which uses both second and third generation sequencing reads
By BioStar 1664 days agogithub.com - HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of...MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads
By Abhi 445 days agogithub.com - MitoHiFi v3.2 is a python pipeline distributed under MIT License ! MitoHiFi was first developed to assemble the mitogenomes for a wide range of species in the Darwin Tree of Life Project...RATT
By Jitendra Narayan 3212 days agoratt.sourceforge.net - RATT is software to transfer annotation from a reference (annotated) genome to an unannotated query genome. It was first developed to transfer annotations between different genome assembly versions. However, it can also transfer annotations between...Hagfish - assess an assembly through creative use of coverage plots
By Abhi 3108 days agogithub.com - Hagfish is a tool that is to be used in data analysis of Next Generation Sequencing (NGS) experiments. Hagfish builds on the concept of coverage plots and aims to assist (amongst others) in quality control of de novo genome assembly or...PANDASEQ
By Shruti Paniwala 2861 days agoneufeldserver.uwaterloo.ca - PANDASEQ assembles paired-end Illumina reads into sequences, trying to correct for errors and uncalled bases. The assembler reads two files in FASTQ format with quality information. If amplification primers were used (e.g., to isolate a variable...Protocol for De novo Genome Assembly using Illumina Reads
By BioStar 1406 days agoIn this protocol, we address and describe the de novo assembly method for small to medium-sized genomes.MyPro: A seamless pipeline for automated prokaryotic genome assembly and annotation
By Neel 2900 days agowww.sciencedirect.com - MyPro is an improved genomics software pipeline for prokaryotic genomes. MyPro is user-friendly and requires minimal programming skills. High-quality prokaryotic genome assembly and annotation can be obtained with ease. It performed better than de...DIAL
By Abhimanyu Singh 2824 days agowww.bx.psu.edu - A computational pipeline for identifying single-base substitutions between two closely related genomes without the help of a reference genome. DIAL works even when the depth of coverage is insufficient for de novo assembly, and it can be extended to...funannotate: Eukaryotic Genome Annotation Pipeline
By Jit 2257 days agogithub.com - Funannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time to accomodate larger genomes. The impetus for this...coursera genome assembly tutorial
By Jit 2555 days agogithub.com - Solutions to Coursera Genome Sequencing (Bioinformatics II)
