Results for "Genome STRiP"
Top-level pages
Reformat is a member of the BBMap/BBTools package. It is a multipurpose tool designed for converting reads or other...al flag "-Xmx2g". For example, to change the line-wrapping length on the human genom...2706 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
Commercial tools Strand NGS offers many different tools incl...d text files Supports custom genome builds and annotation databas...gzipped or not; no reference genome required; read pairs can be g...SnpEff Input: BAM Reference Genome: FASTA indexed with SAMtools...alf, CNV file -cnv Reference genom...2901 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 D...have been copied to another region of the genome.Interspersed RepeatsProcessed...nes which have been reintegrated into the genom...2203 days ago
- alignment: the mapping of a raw sequence read to a location within a reference genome. The mapping occurs because t...equence read to the reference genome. Three core abbreviations are...c variants. RNAME: reference genome identifier (also known as the...e sequence Referencesequence/genom...
2861 days ago
Genome Assembly Tools and Software - PART1 !!
...reported for the assembly of genomes while the others are designed aiming at handling complex genomes. TriMetAss 1.2 – Th...alable and fully parallelized Genome Assembler There is a growi...er designed to assemble virus genomes that have no repeat sequence...Phusion 2.1c – Assembly Genom...2678 days ago
Quick next generation sequencing (NGS) terms definition
fragment size: the Illumina WGS protocol generates paired-end reads from both ends...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 genom...2514 days ago
Alignment-free sequence comparison tools available for next-generation sequencing data analysis
kallisto Transcript abundance quantification from RNA-seq d...https://github.com/bioinfo-ut/GenomeTester4/ Phy-Mer Reference-i...SNPs (dbSNP and Affymetrix's Genome-Wide Human SNP Array) from ra...., ONT or PacBio reads, draft genomes) Software (Perl) https://g...ol for MLST directly from the genom...2363 days ago
- When you have both Illumina and Nanopore data, then SPAdes remains a good option for hybrid assembly - SPAdes was u...pades.py will show you the options: spades.py This produces: SPAdes genom...
2343 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&n...es and reveal cell-type-specific expression changes in type 2 diabetes http://genom...2343 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...or annotating fully sequenced genom...2324 days ago
