Jit
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AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
By Manisha Mishra 3033 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...EAGLER: a scaffolding tool for long reads.
By Jit 2985 days agogithub.com - EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of long reads. The long reads are used to extend the contigs present in the NGS draft and possibly join overlapping...Converting a VCF into a FASTA given some reference !
By Jit 2939 days agoconverting a VCF file into a FASTA file given a reference sequenceSKESA: strategic k-mer extension for scrupulous assemblies
By Jit 2822 days agogithub.com - SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit shows that SKESA produces assemblies that have high sequence quality and contiguity,...Versatile genome assembly evaluation with QUAST-LG
By Jit 2785 days agocab.spbu.ru - QUAST-LG is an extension of QUAST intended for evaluating large-scale genome assemblies (up to mammalian-size). QUAST-LG is included in the QUAST package starting from version 5.0.0 (download the latest release). Run QUAST as...DECIPHER
By Anjana 3597 days agodecipher.cee.wisc.edu - DECIPHER is a software toolset that can be used to maintain, analyze, and decipher large amounts of DNA sequence data. To install DECIPHER, see the Downloads page. To begin using DECIPHER read the "Getting Started DECIPHERing" tutorial. Refer to the...Beagle
By Jit 3570 days agofaculty.washington.edu - Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection. Beagle version 4.1 has a more accurate genotype phasing algorithm and a very fast and...JCVI:Python utility libraries on genome assembly, annotation and comparative genomics
By Jit 2333 days agogithub.com - Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics. https://github.com/tanghaibao/jcvi More at https://github.com/tanghaibao/jcvi/wikiART: Set of Simulation Tools
By Jit 3563 days agowww.niehs.nih.gov - ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated...HASLR: a hybrid assembler which uses both second and third generation sequencing reads
By BioStar 2285 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...
