Genome Assembly Tools and Software - PART1 !!
The genome assemblers generally take a file of short sequence reads and a file of quality-value a...sing Reference and Paired-end Reads misFinder is a tool that a...ta sets containing only short reads from Illumina sequencing or a...which are called from the NGS reads, and aligns the assembled con...2686 days ago
Quick next generation sequencing (NGS) terms definition
...protocol generates paired-end reads from both ends of longer fragments...Most (>90%) of paired-end reads are sampled from no-SV regions, th...rdant read pair is considered discordant. Note that, by definitio...ure produced by these type of reads is known as read-pair signatu...2522 days ago
2489 days ago
Alignment-free sequence comparison tools available for next-generation sequencing data analysis
kallisto Transcript abundance qua...les of the RNA-seq paired-end reads Software (Java) https://git...irectly from raw NGS sequence reads by counting unique k-mer...ird-generation long and noisy reads (10 kbp) using a dimensionali...classification of metagenomic reads to known bacterial genomes us...2371 days ago
2351 days ago
Tools for bacterial whole genome annotation
RAST – Web tool (upload contigs), uses the subsystems in the SEED databa...tigs and estimates the sizes of gaps between them; (ii) IMAGE uses paired-end reads to extend contigs and close g...2332 days ago
Run miniasm assembler on nanopore reads !
Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read sel...he per-base error rate is similar to the raw input reads. Find the detail of the read...2330 days ago
BBSplit: Read Binning Tool for Metagenomes and Contaminated Libraries
BBSplit internally uses BBMap to map reads to multiple genomes at once,...you want to determine whether reads are mouse or human, it does n..., either quantifying how many reads go to each reference, or spli...file for each of them. Paired reads will always be kept together....2314 days ago
2305 days ago
List of visualization tools for genome alignments
Genome browsers are useful not only for showing final re...r.htm JVM Java Visual Mapping tool for NGS reads http://www.springer.com/cda/...nments of huge-scale single-end and pair-end short reads http://omictools.com/mapview...2284 days ago