Results for "read depth"
Top-level pages
Subprocess is one of simplest way of running linux command from within python code Example: if you want to run f...en(["fastqc","-f","fastq","-o", "/home/name/result/","/dev/stdin"],stdin=fopen("read....3542 days ago
A guide for complete R beginners !
This tutorial is intended to introduce users quickly to the basics of R, focusing on...ct.org/ Check out the ‘introduction to R’, which is a much more in depth guide . Also R has a built-i...3355 days ago
Software packages for next gen sequence analysis
...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 gathered through 454 sequenc...nd viewing modes; low or high-depth read pileups; and easy visual...3236 days ago
- Reformat is a member of the BBMap/BBTools package. It is a multi...terleaved files It is multithreaded and can process data at ove...pling (to a fraction of input reads, or an exact number of reads...ally use a shortcut if paired read files have the same name with...to/bbmap/current/ jgi.ReformatReads...
2707 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
...- predicts indels, uses split read alignment profiles, validated...equencing data” Input: depth file generated by DFExtract...ve, variant detection for low-depth targeted NGS data; python mod...ut: CRAVAT report- MS Excel spreadsheet or tab-separated file (em...2902 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...2205 days ago
- Linux Commands Cheat Sheet File System ls — list items in cu... 7 — full permissions 6 — read and write only 5 — read...
2867 days ago
- ...very low probability that the reads in your sample support a TT...t from Damian Gregory Allis. read-length: the number of base pa...dividual sequence read. read-depth: the number of sequence reads...cation. For example, 30X read-depth coverage indicates that the g...
2862 days ago
Genome Assembly Tools and Software - PART1 !!
...sing Reference and Paired-end Reads misFinder is a tool that...t extremely high and variable depth. SFA-SPA 0.2.1 –...Minia 2.0.3 – Short-read Assembler based on a de Bruij...of non-chimeric contigs from read data that has been sequenced f...2679 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...2652 days ago
