Genome Assembly Tools and Software - PART1 !!
...reference bias as compared to mapping based approaches. Tran...cy comparable to conventional mapping based pipelines (see evaluati...ituations that may arise when mapping contigs to the reference geno...rence genome. This is done by mapping the contigs onto the referenc...2695 days ago
Quick next generation sequencing (NGS) terms definition
fragment size: the Illumina WGS protocol generates paired-end reads from both...from a normal distribution. Therefore, in the absence of structural variants, mapping locations of the paired ends...2531 days ago
Phylogenetic & Molecular Genetics Terms and Definitions
analog -- A feature that appears similar in two taxa which have originated from two...g sequence isolated at random from a cDNA library, used for identification and mapping of coding sequences, for disc...2471 days ago
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BBSplit: Read Binning Tool for Metagenomes and Contaminated Libraries
BBSplit internally uses BBMap to map reads...This is different than with ordinary mapping. If a genome (say, human) con...ains an exact repeat somewhere, reads mapping to it will be mapped ambiguou...BBSplit is a tool that bins reads by mapping to multiple references simult...2324 days ago
List of visualization tools for network biology
Network analysis is any structured technique used to mathematically analyze a...es http://www.cs.helsinki.fi/group/sysfys/software/rematch/ SNOW Gene mapping on a reference or human prote...2297 days ago
List of visualization tools for genome alignments
Genome browsers are useful not only for showing fin...ych.uic.edu/DNannotator.htm JVM Java Visual Mapping tool for NGS reads http://ww....broadinstitute.org/igv/ ZOOM Lite NGS data mapping and visualization software h...2293 days ago
Some useful Bioinformatics links
Reference-free prediction of rearrangement breakpoint reads | Bioinformatics | Oxf...matics.biomedcentral.com/articles/10.1186/1471-2105-15-302 Fast and sensitive mapping of nanopore sequencing reads...2251 days ago
Frequent Paired-end reads (PE 2x100) mapping command lines
bowtie2 -x hs37m -X 650 -q -1 r1.fq -2 r2.fq -S r12.bowtie2.sam bwa aln hs37m.fa r1.fq > r1.sai && bwa aln hs37m.fa r2.fq > r2.sai \ &&...2191 days ago
List of non-commercial NGS genotype-calling software
Meaningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and geno...re for imputation and phasing, including a mode for genotype calling. Requires fine-sc...2105 days ago