Results for "3D Genome"
Top-level pages
...ong sequences, Reformat will need more memory; just add the additional flag "-Xmx2g". For example, to change the line-wrapping length on the human genome (which has individual sequenc...2727 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
...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 genome: -refgene (created in MATLAB,...2922 days ago
Tools for Searching Repeats And Palindromic Sequences
...the mid 1960's scientists discovered that many genomes contain stretches of highly...that have been copied to another region of the genome.Interspersed RepeatsProcessed...NA genes which have been reintegrated into the genome with the assitance of a rever...2224 days ago
- ...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...
2882 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...er designed to assemble virus genomes that have no repeat sequence...Phusion 2.1c – Assembly Genome Sequences from Whole Genome S...2699 days ago
Quick next generation sequencing (NGS) terms definition
...a read pair is called concordant if they can be mapped to the reference genome as “expected”: (a...ature.split reads: a read that can only be mapped to the reference genome by breaking into two sub-read...2535 days ago
Alignment-free sequence comparison tools available for next-generation sequencing data analysis
...C) https://github.com/bioinfo-ut/GenomeTester4/ Phy-Mer Reference-i...nown SNPs (dbSNP and Affymetrix's Genome-Wide Human SNP Array) from ra...(e.g., ONT or PacBio reads, draft genomes) Software (Perl) https://g...d tool for MLST directly from the genome sequencing reads Software (P...2384 days ago
- ...agilis assembly by Mick Watson’s group. Again, running spades.py will show you the options: spades.py This produces: SPAdes genome assembler v3.10.1 Usage: /...
2364 days ago
Single Cell RNAseq data analysis tutorial !!
...87775 Single cell transcriptomes identify human islet cell signatures and reveal cell-type-specific expression changes in type 2 diabetes http://genome.cshlp.org/content/early/2016/...2364 days ago
Tools for bacterial whole genome annotation
...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...2345 days ago
