Next Generation Sequencing (NGS)
https://en.wikipedia.org/wiki/Sequencing
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Cutadapt
By Bulbul 2879 days agocutadapt.readthedocs.io - Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Cutadapt helps with these trimming tasks by finding the adapter or primer sequences in an...HTSlib
By Jit 2788 days agohttp://www.htslib.org/ - Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: SamtoolsReading/writing/editing/indexing/viewing SAM/BAM/CRAM formatBCFtoolsReading/writing BCF2/VCF/gVCF files and...Fastq format
By Jit 2739 days agoen.wikipedia.org - FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. Both the sequence letter and quality score are each encoded with a...
Quick next generation sequencing (NGS) terms definition
Last updated 2702 days ago by Neelfragment size: the Illumina WGS protocol generates paired-end reads from both ends of longer fragments. The lengths of these fragments are assumed to be sampled from a normal distribution. Therefore, in the absence of structural variants,...PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool
By Jit 2527 days agohttps://plast.inria.fr/ - PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms. Relying on unique software architecture,...Ranbow: a haplotype assembler for polyploid genomes
By Jit 2345 days agowww.molgen.mpg.de - Ranbow is a haplotype assembler for polyploid genomes. It has been developed for the haplotype assembly of the hexaploid sweet potato genome, which is highly heterozygous. Ranbow can also be applied to other polyploid genomes. After a first phasing,...Installing Salmon for Trinity !
By Rahul Nayak 2313 days ago Comments (1)Installing Trinity dependencies !-
List of non-commercial NGS genotype-calling software
Last updated 2276 days ago by Jit Comments (1)Meaningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and genomics studies, relies crucially on the accurate calling of SNPs and genotypes. Recently developed statistical methods both improve and... AMStat: display statistics of large sequence files from next generation sequencing projects
By Neel 2183 days agosamstat.sourceforge.net - SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects. When applied to SAM/BAM files all statistics are reported for unmapped, poorly and accurately mapped reads...Introduction to Bioinformatics
By eliabrodsky 1975 days agoLearn about bioinformatics online by watching videos, reading engaging articles and practicing bioinformatics skills using public domain datasets.
