Tag Archives: FASTQ

Illumina FASTQ files – Read Segment Quality Control Indicator

Posted on April 30, 2010 by Peter

In another quirk to the FASTQ story, recent Illumina FASTQ files don’t actually use the full range of PHRED scores – and a score of 2 has a special meaning, The Read Segment Quality Control Indicator (RSQCI, encoded as ‘B’). … Continue reading →

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BioRuby 1.4.0 released

Posted on December 29, 2009 by Naohisa Goto

We are pleased to announce the release of BioRuby 1.4.0. This new release contains many new features, in addition to bug fixes and improvements. PhyloXML support: Support for reading and writing PhyloXML file format is added, developed by Diana Jaunzeikare, … Continue reading →

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Sanger FASTQ format and the Solexa/Illumina variants

Posted on December 17, 2009 by Peter

I’m delighted to announce an open access publication in Nucleic Acids Research describing the FASTQ file format based on the conventions agreed by the OBF projects: The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ … Continue reading →

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Interleaving paired FASTQ files with Biopython

Posted on December 14, 2009 by Peter

This post is about paired end data (FASTA or FASTQ) and manipulating it with Biopython’s Bio.SeqIO module (see also FASTQ conversions & speeding up FASTQ).

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BioPerl 1.6.1 released

Posted on September 29, 2009 by Chris Fields

We are pleased to announce the immediate availability of BioPerl 1.6.1, the latest release of BioPerl’s core code. You can grab it here: Via CPAN: http://search.cpan.org/~cjfields/BioPerl-1.6.1/ Via the BioPerl website: http://bioperl.org/DIST/BioPerl-1.6.1.tar.bz2 http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz http://bioperl.org/DIST/BioPerl-1.6.1.zip The PPM for Windows should also finally … Continue reading →

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Working with FASTQ files in Biopython when speed matters

Posted on September 25, 2009 by Peter

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. Continue reading →

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Simpler, optimized format conversion with Biopython

Posted on September 22, 2009 by davidw

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. Continue reading →

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Indexing sequence files with Biopython

Posted on September 21, 2009 by Peter

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. Continue reading →

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Biopython 1.51 released

Posted on August 17, 2009 by davidw

We are pleased to announce the release of Biopython 1.51.This new stable release enhances version 1.50 (released in April) by extending the functionality of existing modules, adding a set of application wrappers for popular alignment programs and fixing a number … Continue reading →

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Biopython 1.51 beta released

Posted on June 23, 2009 by Peter

A beta release for Biopython 1.51 is now available for download and testing. In the two months since Biopython 1.50 was released, we have introduced support for writing features in GenBank files using Bio.SeqIO, extended SeqIO’s support for the FASTQ … Continue reading →

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