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I am using this perl code right nowadays.#!/usr/bin/perl use warnings; use strict;open(FASTA, "<", seq.fa) or die("Can't open\n"); my %singleLineSequences; my $sequence_id; while(){ my $line = $_; chomp($line); if ($line =~...

A Compendium of Clean Graphs in R http://shinyapps.org/apps/RGraphCompendium/index.php

De #Bruijn #Graph #assembly http://www.cs.jhu.edu/~langmea/resources/lecture_notes/assembly_dbg.pdf

Extract reference nucleotide from BAM file: samtools view your.bam | awk '{print substr( $10, 100, 1)}' #SAM #BAM #Samtools #Tricks #NGS

Samtool WIKI http://davetang.org/wiki/tiki-index.php?page=SAMTools

SAM file description https://samtools.github.io/hts-specs/SAMv1.pdf

SAM flags https://gist.github.com/davfre/8596159

Decoding SAM flags This utility makes it easy to identify what are the properties of a read based on its SAM flag value, or conversely, to find what the SAM Flag value would be for a given combination of properties. To decode a given SAM flag...

#Extract #Chromosome #Number And Start Position #Reads: samtools view bamfile.bam|awk '{print $3 "\t" $4 "\t" $4+length($10)-1}' > newfile.tab

The greengenes web application provides access to the 2011 version of the greengenes 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading. The data and tools presented by greengenes can assist the researcher in choosing...

CSBB is a command line based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R and python in background for specific modules....

Kaiju is a program for the taxonomic classification of metagenomic high-throughput sequencing reads. Each read is directly assigned to a taxon within the NCBI taxonomy by comparing it to a reference database containing microbial and viral protein...

Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster...

Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers) at distal genomic locations can interact with each other via chromatin folding and affect gene expression levels. Genomic technologies for...

#NGS basics http://deeptools.readthedocs.io/en/latest/content/help_glossary.html #Tutorial #Help

alignment: the mapping of a raw sequence read to a location within a reference genome. The mapping occurs because the sequences within the raw read match or align to sequences within the reference genome. Alignment information is stored in the SAM...