Abhimanyu Singh
A bioinformatics beginner
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AGORA: Algorithm for Gene Order Reconstruction in Ancestors
By Jit 1467 days agogithub.com - AGORA stands for “Algorithm for Gene Order Reconstruction in Ancestors” and was developed by Matthieu Muffato in the DYOGEN Laboratory at the École normale supérieure in Paris in 2008. // | | // ) ) // ) )...CAMSA :: a tool for Comparative Analysis and Merging of Scaffold Assemblies
By Rahul Nayak 2991 days agohttps://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...Metassembler: merging and optimizing de novo genome assemblies
By Rahul Nayak 2860 days agosourceforge.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...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,...Rebaler: program for conducting reference-based assemblies using long reads.
By Jit 2727 days agogithub.com - Rebaler is a program for conducting reference-based assemblies using long reads. It relies mainly on minimap2 for alignment and Racon for making consensus sequences. I made Rebaler for bacterial genomes (specifically for the...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...Minipolish: A tool for Racon polishing of miniasm assemblies
By BioStar 2286 days agogithub.com - Miniasm is a great long-read assembly tool: straight-forward, effective and very fast. However, it does not include a polishing step, so its assemblies have a high error rate – they are essentially made of stitched-together pieces of long...merqury: Evaluate genome assemblies with k-mers
By Jit 2073 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...Syri compares alignments between two chromosome-level assemblies and identifies synteny and...
By Shruti Paniwala 1375 days agogithub.com - Syri compares alignments between two chromosome-level assemblies and identifies synteny and structural rearrangements.
