Results for "genome assembly"
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 genome (...2712 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
...rkflow, read mapping, de novo assembly, variant detection, RNA-Seq, ChIP-Seq, Genome Browser, etc (entire list on...reference genome or de novo assembly not needed Output: LoFr...SnpEff Input: BAM Reference Genome: FASTA indexed with SAMtools fa...2907 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 w...2210 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/genome&n...
2867 days ago
Genome Assembly Tools and Software - PART1 !!
...e therefore list many genomle assembly tools here. We mainly reported for the assembly of genomes while the others are designed aiming at handling complex genomes. TriMetAss 1.2 – Th...OMWare 1.0 – Efficient Assembly of Genome-wide Physical Maps The p...2684 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 b...2521 days ago
Alignment-free sequence comparison tools available for next-generation sequencing data analysis
...tps://github.com/lh3/minimap Assembly De novo genome assembly MHAP Produces highly cont...., ONT or PacBio reads, draft genomes) Software (Perl) https://git...ol for MLST directly from the genome sequencing reads Software (Pyt...stances between them based on assembly using de Bruijn graphs and Br...2369 days ago
- ...ains a good option for hybrid assembly - SPAdes was used to produce the B fragilis assembly by Mick Watson’s g...This produces: SPAdes genome assembler v3.10.1 Usage: /us...utput in folder “hybrid_assembly”...
2349 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://genome.c...2349 days ago
Tools for bacterial whole genome annotation
..., as well as other functional genome units such as structural RNAs...or annotating fully sequenced genomes. PAGIT: Provides a toolkit...ome assemblies created via an assembly software. PAGIT compiled four...gh-quality prokaryotic genome assembly and annotation. It was valida...2330 days ago
