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Remove the unwanted characters from Fasta file: sed -e '/^[^>]/s/[^ATGCatgc]/N/g' infile.fa #sed #unwanted #illegal #remove #correct #fasta #linux

Remove the fasta with zero size: awk 'BEGIN {RS = ">" ; FS = "\n" ; ORS = ""} $2 {print ">"$0}' input.fas > output.fas #fasta #remove

Other tools focus on getting data out of the fastq or fast5 files, which is slow and computationally intensive. The benefit of this approach is that it works on a single, small, .txt summary file. So it's a lot quicker than most other things out...

dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs...

Bioinformatics JRF at IIT https://www.iitr.ac.in/administration/uploads/File/bt/2017/adv30112017.pdf #JRF

PeerJ also accept bioinformatics papers https://peerj.com

PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms. Relying on unique software architecture,...

scripts to parse and analyse MCScanX collinearity output

Scripts for the analysis of HGT in genome sequence data

phyloXML (example) is an XML language designed to describe phylogenetic trees (or networks) and associated data. PhyloXML provides elements for commonly used features, such as taxonomic information, gene names and identifiers, branch...

Ribbon can be used for long reads, short reads, paired-end reads, and assembly/genome alignments. Instructions for each data format are available by clicking on "instructions" in each tab on the right. Local installation: You can install Ribbon...

Computational Biology is a huge field of study, that touches upon many distinct algorithmic and biological areas of study. What we are able to cover in this course will depend, in part, on the pace at which we move, which I will attempt to...

The primary goal of the course is for students to be grounded in theory and leave the course empowered to conduct independent genomic analyses. We will study the leading computational and quantitative approaches for comparing and analyzing...

Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used...

Linux command to find the file contains a string "LOCK_EX": grep -Ril "LOCK_EX" / #Root #Find #Linux #Grep #search

simNGS is software for simulating observations from Illumina sequencing machines using the statistical models behind the AYB base-calling software. By default, observations only incorporate noise due to sequencing and do not incorporate effects from...

RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, quality control, read alignment,...

A major breakthrough (replaced microarrays) in the late 00’s and has been widely used since Measures the average expression level for each gene across a large population of input cells Useful for comparative transcriptomics,...

"DRAWID has number of advantages including a user-friendly interactive interface, possibility for simultaneous chromosome and FISH/GISH/banding signal measurement and idiogram drawing as well as number of useful functions facilitating the procedure...

You should try installing  pip install futures Futures feature has never included in Python 2.x core. However, it's present in Python 3.x since Python 3.2.