Category Archives: Release

Long read patching is now even easier

Using long reads for patching is now fully integrated into the ALLPATHS-LG pipeline – manual data preparation is no longer required. Please download the latest release (37843 or above) and the accompanying manual that describes how to incorporate long reads into your … Continue reading

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ALLPATHS-LG much faster with Transparent Huge Pages

Starting with version 2.6.38, the Linux kernel allows for Transparent Huge Pages (THP), a mechanism whereby memory pages of size 2MB are used in ‘situations where they would be useful’, rather than the standard 4KB pages. We have found that … Continue reading

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Stringency of long read patches increased

ALLPATHS-LG will patch gaps in scaffolds using long reads from PacBio. As of revision 37660 we have tightened up the join process so that long reads having longer overlaps with their neighboring contigs are given more weight. This leads to … Continue reading

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PacBio/Illumina gap patching in ALLPATHS-LG now faster

As of revision 37655, the algorithm that computes the consensus of PacBio reads that patch a gap between ‘Illumina’ contigs is now ~100 times faster. For bacterial genomes it was taking several hours. The speedup was obtained by replacing an … Continue reading

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Better handling of asymmetric library distributions

The distribution of jumping library fragment (“insert”) sizes can be far from Gaussian. Despite this, assemblers often model these distributions as Gaussian, leading to errors and inaccuracies. As of revision 37618,  ALLPATHS-LG calculates the actual pair separation distribution for all libraries … Continue reading

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New feature! Gap patching using long reads

For bacterial-sized genomes, ALLPATHS-LG now accepts an additional data type as input: long reads (for example from Pacific Biosciences), and uses these reads to patch gaps in scaffolds obtained from short reads.  We recommend using high coverage (e.g. 25-100x) by … Continue reading

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Example data now available for download

We have prepared a small example data set to help test your ALLPATHS-LG installation and to provide guidance on how to prepare your own data. Download test.genome.tar.gz from our FTP site here and then follow the instructions provided.

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ALLPATHS-LG faster now

Revision 36405 includes a faster version of error correction, that also reduces i/o usage. In combination with a recent speedup of the “fragment filling” module, ALLPATHS-LG is now about 20% faster.

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Improved handling of polymorphism

Revision 35887 introduces some changes that improve the performance of ALLPATHS-LG on polymorphic data sets. On a 10 Mb human test region, the N50 contig size is now 81 kb, roughly double what it was before. More changes are in … Continue reading

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ALLPATHS-LG adds support for Fastq and Fasta files.

By popular demand, ALLPATHS-LG can now import sequence data in Fastq and Fasta format – in addition to the already supported BAM format. Full details of how to import BAM, Fastq and Fasta files can be found in the updated … Continue reading

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