Results for "structural and sequence variation"
Blogs
Basic command-line to run BLAST
The goal of this tutorial is to run you through a demonstration of the command line, which you may not have...tein.faa This grep command uses the c flag, which reports a c...[-html] [-max_target_seqs num_sequences] [-num_threads int_value] [-...[-html] [-max_target_seqs num_sequences...2383 days ago
- LiftOver is a necesary step to bring all genetical analysis to... Convert both genome position and dbSNP rs number over differen...follow: Deleted in new: Sequence intersects no chains Partially deleted in new: Sequence insufficiently intersects one...6497-6497 from hg19 to GRch38 and it re...
2298 days ago
List of motif discovery tools !
In genetics, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a bi...significance. For proteins, a sequence motif is distinguished from a structural motif, a motif formed...e topography of proteins with structural and topographi...2132 days ago
Understanding reads mapping and flags !
...a read to a single reference sequence that may include insertions, deletions, skips and clipping, but may not in...meric reads are indicative of structural variation in DNA-seq and it may indica...a RealignerTargetCreator and IndelRealigner. (WARNING: I am not...1975 days ago
- This is an extract of taxdump-readme.txt to be found at ftp://f...contain taxonomic information and are briefly described below....by "\t|\n" (tab, vertical bar, and newline) characters. Each rec...-- 1 if this subtree has no sequence data yet comments -- free-text comments and citat...
1687 days ago
10 NGS services companies around the globe !
...ular diagnostics laboratories and consumer genomics companies....that allow access to genomic sequence information. The C...cas, Europe, Asia, Australia, and the Middle-East &Africa t...iotech AG was founded in 1990 and is headquartered in Constance, Ger...ries, namely, BGI China (Mainland), BGI...1398 days ago
Bioinformatics tools for telomere to telomere assembly !
...;– k-mer-based assembly and variant calling evaluation for impro...nerate high-quality consensus sequences from HiFi reads (Zev Kr...polymorphic sites within the sequences and removing potential chime...ols for filtering, comparing, and annotating structural variant (SV) calls in VCF fo...1130 days ago
Protocol for De novo Genome Assembly using Illumina Reads
...g a large number of short DNA sequences and placing them back together to...utshell the protocol: Get the sequence file(s) read from the sequenc...have an idea of what you have and what the standard is like. If requ...AP is also useful for finding structural variants between genomes fr...1343 days ago
Frequently used bioinformatics tools for viral genome analysis !
...aluation of genome assemblies and assembly algorithms. Salzberg...Kraken: ultrafast metagenomic sequence classification using exact al...46 (2014). MUMmer: Versatile and open software for comparing large...9, e57 (2011). SAMtools: The Sequence Alignment/Map format and SAMto...1186 days ago
Illumina based assembly pipeline steps !
Illumina Merge re-sequenced FastQ files (cat) Read QC (Fast...ad alignment (Bowtie 2) Sort and index alignments (SAMtools) Primer sequence removal (iVar; ampli...icard, SAMtools) Genome-wide and amplicon coverage QC plots (mosdep...variant calling and consensus sequence generation routes (iVar varia...1016 days ago
