1. Ktrim: An extra-fast, accurate adapter trimmer for sequencing data. It processes FASTQ files from multiple lanes with minimal mismatching and over-trimming of adapters.2. BWA MEM: A reliable alignment tool (particularly for mapping ALT contigs...
The 3rd Annual Next Generation Sequencing Asia Congress is to be held on the 22nd and 23rd of October 2013 in Singapore. Over the 2 days, the conference will provide an overview of the current options of next-generation sequencing platforms,...
There are numerous genome assembly tools available, each with its strengths and weaknesses. Here is a list of some widely used genome assembly tools as of my last update in September 2021:
SPAdes: An assembler specifically designed for...
github.com - Mix is a tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices...
github.com - MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome...
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
There are many R software and bioconductor packages for NGS data analysis, some of them are as follows
Biostrings
The Biostrings package from Bioconductor provides an advanced environment for efficient sequence management and analysis in R. It...
www.gigasciencejournal.com - Bioinformatics software varies greatly in quality. In terms of usability, the command line interface is the first experience a user will have of a tool. Unfortunately, this is often also the last time a tool will be used. Here I present ten...