UNIX Archives - CVR Bioinformatics

A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml

November 15, 2017
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A wide range of formats exist for representing the comparisons of different sequences to each other: blast tabular, blast xml, psl, pslx, SAM/BAM, BED Most of these formats can be converted from one format to another. Sometimes the format is lossless allowing for the original data to be perfectly converted without the loss of information. […]

July 19, 2017
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FAST5 format from Oxford Nanopore (ONT) is in fact HDF5, which is a very flexible data model, library, and file format for storing and managing data. It is able to store an unlimited variety of datatypes. A number of tools have been developed for handling HDF5 available from here. The most useful are: hdfview, a […]

August 10, 2016
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We have shared our knowledge on Viral bioinformatics and genomics with yet another clever and friendly bunch of researchers. Sixteen delegates from across the world joined us for a week of intensive training. The line-up of instructors changed slightly due to the departure of Gavin Wilkie earlier in the year. Instructors: Joseph Hughes (Course Organiser) […]

April 25, 2016
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Sequence runs on NGS instruments are typically carried out with multiple samples pooled together. An index tag (also called a barcode) consisting of a unique sequence of between 6 and 12bp is added to each sample so that the sequence reads from different samples can be identified. On the Illumina MiSeq, the process of demultiplexing […]

April 20, 2016
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I use NCBI Entrez Direct UNIX E-utilities regularly for sequence and data retrieval from NCBI. These UNIX utils can be combined with any UNIX commands. It is available to download from the NCBI website: ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/ A few useful examples for NCBI edirect utilities. Download a sequence in fasta format from NCBI using accession number esearch -db […]

April 1, 2016
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These are the steps I used to create a batch of bootable BioLinux Live USB sticks – with persistent data so that any data files created/downloaded would be preserved. This was used for a course so that each stick had the same NGS data and the same additional (non-BioLinux) programs pre-installed and already configured. Step 1 […]

April 1, 2016
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Imagine having two different servers called darwin and linnaeus. Imagine that darwin is a great server with loads of RAM for doing de-novo assembly and that linnaeus has loads of nodes so a great server for splitting up jobs and running lots of jobs in parallel. To make good use of all these resources, it […]

October 14, 2015
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All bioinformatics server users and administrators would know how easy it is to fill up our home directories with huge amounts of data, especially when you are analysing deep sequencing data on a daily basis. Here is a list of a few useful commands and tips that can help to keep your home directory tidy. […]

August 18, 2015
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The first Viral Bioinformatics and Genomics training course held at the University of Glasgow was completed successfully by 14 delegates (nine external and five internal) on 10-14 August 2015. The course took place in the McCall Building computer cluster, and the adjacent Lomond and Dumgoyne Rooms were used for refreshments and lunch. Instructors: Joseph Hughes […]

June 12, 2015
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Basic Local Alignment Search Tool (BLAST) is one of the most commonly used programs for sequence classification using similarity search. Standalone BLAST can be setup easily on the local server. More info about how to set it up on a local Linux server can be found here: http://www.ncbi.nlm.nih.gov/books/NBK52640/ In our lab, all our servers run […]

Archives

A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml

Exploring the FAST5 format

2nd Viral Bioinformatics and Genomics Training Course (1st – 5th August 2016)

How to demultiplex Illumina data and generate fastq files using bcl2fastq

NCBI Entrez Direct UNIX E-utilities

How to make a BioLinux Live USB Stick – with persistent data storage

Submitting a job to run on another server and retrieving the results

Top tips to keep your home folder on a server tidy

1st Viral Bioinformatics and Genomics Training Course

Setting up automatic BLAST database update on linux servers

Training Courses