![]() ![]() Linux command line exercises for NGS data processing by Umer Zeeshan Ijaz.Bioinformatic one-liners by Stephen Turner.They can be done locally in your command line and don't require any clumsy dependancies. This section first starts off with some quick useful commands that will be helpful to assess and manipulate your fasta and fastq file. Below are just two on the most useful ones that I like (I tend to like the command line interface ones, as they can easily be upscaled and used on your VM/supercomputer if needed). Some use the command line interface, there is also plenty of GUI and web-based programs too. This is to cover off on some basic quick command line tools to work with sequence data (mainly written for fasta and fastq format but generally useful for most types of sequence files. Quick commands for manipulating sequence files Muscle -maketree -in seqs_muscle.afa -out seqs_muscle_tree.phy -cluster neighborjoining Make an alignment and save to a file in FASTA format: ![]() In most cases, only a few command line options are needed. MUSCLE is one of the most common tools to align sequences. It has a range of features and plugins that allow you to do a wide range of phylogenetic and bioinformatic analysis. Geneious - a paid program, that is one of the most widely used by molecular biologists.GeneStudio - is a collection of free programs that allow you to do everything from viewing & editing sequences to building phylogenies and editing trees.In additional to basic visualisation and sequence editing it has some useful features to deisgn primers (integrated with primer3), sequence alignment (including short reads), contig assembly, phylogenetic trees and more. UGENE - is a free program that allows has a lot more features than the first two programs.It works in a similar fashion to FinchTV and also has a good short cut to BLAST sequences. 4 peaks - another free program, that works well on macOS.It also allows you to do some basic edits on your sequences. FinchTV - a free program, that allows you to quickly and easily visualise your ab1 files.There are lots of programs that you can use to visualise and edit these files. ab1 file is the most useful as it contains the cromatogram which contains information on quality of each base call. When you recieve your raw sanger sequences you will usually recieve files with the following extensions. Quick tips in working with sequence files Viewing ![]()
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