Jit
Enthusiast computational biologist with business dream !!!
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KisSplice
By Jit 3490 days agokissplice.prabi.fr - KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler that allows to identify SNPs, indels and alternative splicing events. It can deal with an arbitrary number...PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM and Look Ahead...
By Rahul Nayak 2832 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...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Jit 2864 days agogithub.com - Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. The algorithm uses an A-Bruijn graph to find the overlaps between reads and does not require them to be error-corrected. After...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Rahul Nayak 2436 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...SALSA: A tool to scaffold long read assemblies with Hi-C
By Jit 2822 days agogithub.com - This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch. To use the latest version,...Merqury: reference-free quality and phasing assessment for genome assemblies
By Jit 2100 days agogithub.com - Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality...RagTag: a collection of software tools for scaffolding and improving modern genome assemblies
By Jit 1638 days agogithub.com - RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include: Homology-based misassembly correction Homology-based assembly scaffolding and patching Scaffold mergingMECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
By Rahul Nayak 2857 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...Protocol for De novo Genome Assembly using Illumina Reads
By BioStar 1875 days agoIn this protocol, we address and describe the de novo assembly method for small to medium-sized genomes.
