Results for "discordant read pairs"
Top-level pages
Software packages for next gen sequence analysis
Integrated solutions * CLCbio Genomics Workbench - de novo and r...X. * SHORE - SHORE, for Short Read, is a mapping and analysis pi...per - GenomeMapper is a short read mapping tool designed for acc...d-end and single-end Illumina reads. Uses a Needleman-Wunsch alg...brid de-novo assemblies using reads...3266 days ago
- Reformat is a member of the BBMap/BBTool...ally use a shortcut if paired read files have the same name with...sample 10% of the first 20000 pairs in an interleaved file: refo...o ensure reads are treated as pairs) Pipe in a gzipped sam file...to/bbmap/current/ jgi.ReformatReads" for example, java -ea -Xmx20...
2737 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
Commercial tools Strand NGS offers...ference genome required; read pairs can be given Output: FASTA...- predicts indels, uses split read alignment profiles, validated...ify SNPs between tumor/normal pairs- predicts probability of diff...ut: CRAVAT report- MS Excel spreadsheet or tab-separated file (em...2932 days ago
Tools for Searching Repeats And Palindromic Sequences
What are genomic interspersed repeats? In the mid 1960's scientists discovered that m...does not matter whether the nucleic acid strand is read starting from the 3' (three p...indromes the sequences on the complimentary strands read...2234 days ago
- Linux Commands Cheat Sheet File System ls — list items in cu... 7 — full permissions 6 — read and write only 5 — read...
2897 days ago
- alignment: the mapping of a raw sequence read to a location within a refere...dicates that the first 5 base pairs of the read align to the reference, followed by 2 base pairs, which are unique to the rea...requently referred to as mate-pairs. QNAME: unique identifier of...
2892 days ago
Genome Assembly Tools and Software - PART1 !!
The genome assemblers generally take a file of short sequence reads and a file of quality-value...equences, using Illumina read pairs sequenced from mixed populat...Minia 2.0.3 – Short-read Assembler based on a de Bruij...of non-chimeric contigs from read data that has been sequenced f...2709 days ago
Source Code and Pseudo Code !!
An algorithm is a procedure for solving a problem in terms of the actions to...first char of string to screen set read character to hold character While next character read != blanks and white space...e and source code too. It really hels the reada...2682 days ago
Perl Special Vars Quick Reference
$_ The default or implicit variable. @_ Subroutine parameters. $a$b...Input / Output layer information. ${^UNICODE} Read-only Unicode settings. $...mplement scoped pragmas. ${^TAINT} Taint mode read-...2667 days ago
Quick next generation sequencing (NGS) terms definition
...protocol generates paired-end reads from both ends of longer fragments...Most (>90%) of paired-end reads are sampled from no-SV regions, th...rdant read pair is considered discordant. Note that, by definition, the discordant read pairs signal potential SVs. The seq...2545 days ago
