Illumina FASTQ files – Read Segment Quality Control Indicator

April 30, 2010 :

In another quirk to the FASTQ story, recent Illumina FASTQ files don’t actually use the full range of PHRED scores […]

BioRuby 1.4.0 released

December 29, 2009 :

We are pleased to announce the release of BioRuby 1.4.0. This new release contains many new features, in addition to […]

Sanger FASTQ format and the Solexa/Illumina variants

December 17, 2009 :

I’m delighted to announce an open access publication in Nucleic Acids Research describing the FASTQ file format based on the […]

Interleaving paired FASTQ files with Biopython

December 14, 2009 :

This post is about paired end data (FASTA or FASTQ) and manipulating it with Biopython’s Bio.SeqIO module (see also FASTQ […]

BioPerl 1.6.1 released

September 29, 2009 :

We are pleased to announce the immediate availability of BioPerl 1.6.1, the latest release of BioPerl’s core code. You can […]

Working with FASTQ files in Biopython when speed matters

September 25, 2009 :

Biopython’s SeqIO interface revolves around SeqRecord objects which can impose a speed penalty. For FASTQ files the quality string gets turned into a list of integers on parsing, and then re-encoded back to ASCII on writing. Working directly with the raw strings is less flexible, but much faster.

Simpler, optimized format conversion with Biopython

September 22, 2009 :

In this post we’ll look at the new convert() function that both Bio.SeqIO and Bio.AlignIO will get in Biopython 1.52. This allows easier file conversion, and internally provides a mechanism for specific optimisations, such as for FASTQ conversions.

Indexing sequence files with Biopython

September 21, 2009 :

The forthcoming release of Biopython 1.52 will include a couple of nice improvements to the Bio.SeqIO module, and here we’re going to introduce the new index function.

Biopython 1.51 released

August 17, 2009 :

We are pleased to announce the release of Biopython 1.51.This new stable release enhances version 1.50 (released in April) by […]

Biopython 1.51 beta released

June 23, 2009 :

A beta release for Biopython 1.51 is now available for download and testing. In the two months since Biopython 1.50 […]