BOL

schneebergerlab.github.io - SyRI is a comprehensive tool for predicting genomic differences between related genomes using whole-genome assemblies (WGA). The assemblies are aligned using whole-genome alignment tools, and these alignments are then used as input to SyRI. SyRI...

github.com - A tool for converting for recovering synteny blocks from multiple alignment (in MAF fromat) This tool is a standalone version of Ragout module [http://fenderglass.github./Ragout]

synvisio.github.io - SynVisio lets you explore the results of McScanX a popular synteny and collinearity detection toolkit and generate publication ready images. SynVisio requires two files to run: The simplified gff file that was used as an...

catchenlab.life.illinois.edu - Chromonomer is a program designed to integrate a genome assembly with a genetic map. Chromonomer tries very hard to identify and remove markers that are out of order in the genetic map, when considered against their local assembly order; and to...

https://cblab.org/camsa/ - CAMSA – is a tool for Comparative Analysis and Merging of Scaffold Assemblies, distributed both as a standalone software package and as Python library under the MIT license. Main features: works with any number of...

sourceforge.net - Metassembler combines multiple whole genome de novo assemblies into a combined consensus assembly using the best segments of the individual assemblies. Genome assembly projects typically run multiple algorithms in an attempt to find the single best...

bitbucket.org - Some parts of a genome may have a very high degree of heterozygosity. This causes contigs for both haplotypes of that part of the genome to be assembled as separate primary contigs, rather than as a contig and an associated haplotig. This can be an...

github.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 merging

ftp.genomics.org.cn - An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE...

ftp.ncbi.nih.gov - Now a days there are a lots of genomics databases available around the world. This bookmark is created to provide all links in one place ... ftp://ftp.ncbi.nih.gov/genomes/ https://hgdownload.soe.ucsc.edu/downloads.html