Results for "Whole genome"
Top-level pages
Reformat is a member of the BBMap/BBTools package. It is a multipurpose tool designe...al flag "-Xmx2g". For example, to change the line-wrapping length on the human genome (which has individual sequenc...2720 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
...aneuploid tumor samples using whole genome sequencing data”...SnpEff Input: BAM Reference Genome: FASTA indexed with SAMtools...for analysis of targeted- and whole genome re-sequencing projects&...alf, CNV file -cnv Reference genome: -refgene (created in MATLAB,...2915 days ago
Tools for Searching Repeats And Palindromic Sequences
What are genomic interspersed repeats? In...960's scientists discovered that many genomes contain stretches of highly...been copied to another region of the genome.Interspersed RepeatsProcessed...which have been reintegrated into the genome with the assitance of a rever...2217 days ago
- alignment: the mapping of a raw seq...sequence reads to a reference genome. BAM Format: binary, compres...equence read to the reference genome. Three core abbreviations are...c variants. RNAME: reference genome identifier (also known as the...e sequence Referencesequence/genome A fully assembled vers...
2875 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 S...ed by the de novo assembly of whole genomes with next-generation s...2692 days ago
Quick next generation sequencing (NGS) terms definition
fragment size: the Illumina WGS protocol generates p...d concordant if they can be mapped to the reference genome as “expected”: (a...bsp;a read that can only be mapped to the reference genome by breaking into two sub-read...2528 days ago
Alignment-free sequence comparison tools available for next-generation sequencing data analysis
...., 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...ol for MLST directly from the genome sequencing reads Software (P...2377 days ago
- When you have both Illumina and Nanopore data, then SPAdes remains a good option for...pades.py will show you the options: spades.py This produces: SPAdes genome assembler v3.10.1 Usage: /...
2357 days ago
Single Cell RNAseq data analysis tutorial !!
A major breakthrough (replaced microarrays) in the late 00’s and has been wi...es and reveal cell-type-specific expression changes in type 2 diabetes http://genome.cshlp.org/content/early/2016/...2357 days ago
Tools for bacterial whole genome annotation
RAST – Web tool (up...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...or annotating fully sequenced genomes. PAGIT: Provides a toolkit...2338 days ago
