2722 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
...gzipped or not; no reference genome required; read pairs can be g...aneuploid tumor samples using whole genome sequencing data”...for analysis of targeted- and whole genome re-sequencing projects”...alf, CNV file -cnv Reference genome: -refgene (created in MATLAB, GISIT...2917 days ago
Tools for Searching Repeats And Palindromic Sequences
What are genomic interspersed repeats? In the mid 1960's scientists discovered that many genomes contain stretches of highly repetitive...ave been copied to another region of the genome.Interspersed RepeatsProcessed...es which have been reintegrated into the genome with...2219 days ago
2877 days ago
Genome Assembly Tools and Software - PART1 !!
...Celera Assembler 8.3 – Whole Genome Shotgun Assembler Ce...fragmentary data produced by whole-genome shotgun sequencing. The...Phusion 2.1c – Assembly Genome Sequences from Whole Genome Shotgun...ed by the de novo assembly of whole genomes with next-generation sequenc...2694 days ago
Quick next generation sequencing (NGS) terms definition
fragment size: the Illumina WGS protocol generates paired-end reads from both ends...concordant if they can be mapped to the reference genome as “expected”: (a...sp;a read that can only be mapped to the reference genome by br...2530 days ago
Alignment-free sequence comparison tools available for next-generation sequencing data analysis
...SNPs (dbSNP and Affymetrix's Genome-Wide Human SNP Array) from ra...., ONT or PacBio reads, draft genomes) Software (Perl) https://g...of sequencing errors in raw, whole genome sequencing reads (k-mer...embled raw sequence data from whole genome sequencing projects; pr...2379 days ago
2359 days ago
Single Cell RNAseq data analysis tutorial !!
A major breakthrough (replaced microarrays) in the late 00’s and has been widely used since Measures the&...s and reveal cell-type-specific expression changes in type 2 diabetes http://genome.cshlp...2359 days ago
Tools for bacterial whole genome annotation
RAST – Web tool (upload contigs), uses the subsyst...ation (if you have only a few genomes to annotate). Prokka &...y useful if you have loads of genomes or need to annotate a pangen..., as well as other functional genome units such as structural RNAs...2339 days ago