Jit
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ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.
By Seema Singh 2446 days agogithub.com - ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set. Detail paper...FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads
By Jit 2334 days agogithub.com - Here is the command to run the tool: python finisherSC.py destinedFolder mummerPath If you are running on server computer and would like to use multiple threads, then the following commands can generate 20 threads to run FinisherSC. python...MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads
By Abhi 492 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...Understanding PacBio
By Jitendra Narayan 2876 days agogithub.com - This tutorial includes resources for learning more about PacBio data and bioinformatics analysis, and includes content suitable for both beginners and experts. Below are links to training modules (webinars and PowerPoint presentations) to help you...Protocol for De novo Genome Assembly using Illumina Reads
By BioStar 1453 days agoIn this protocol, we address and describe the de novo assembly method for small to medium-sized genomes.SViper: Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact...
By Neel 1845 days agogithub.com - Call sviper ~$ ./sviper -s short-reads.bam -l long-reads.bam -r ref.fa -c variants.vcf -o polished_variants This will output a polished_variants.vcf file, that contains all the refined variants. Sometimes it is helpful to look at the...LoRMA: A tool for correcting sequencing errors in long reads
By Abhimanyu Singh 2316 days agogite.lirmm.fr - An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are...CoLoRMap: Correcting Long Reads by Mapping short reads
By Jit 2333 days agogithub.com - Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies....Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de...
By Jit 1958 days agojournals.plos.org - Chromosome-level genome assembler combining multiple de novo assemblies https://github.com/jkimlab/IMAPComparison of Short Read De Novo Alignment Algorithms
By Rahul Agarwal 4159 days agobiochem218.stanford.edu - Excellent article to introduce different sequencing methods along with tools for de novo assembly of sequencing reads and their relevant references. Title: Comparison of Short Read De Novo Alignment Algorithms Author: Nikhil Gopal
