GVL software updates

We’ve just updated the command line tools that are pre-installed on GVL. There are several new ones (both new in general and new to GVL), and lots of version updates to existing tools. The interesting updates are summarized below:

New Tools

centrifuge 1.0.3-beta Fast and accurate taxonomic assignment of reads – NO DATABASE, check brew info centrifuge for build instructions [http://www.ccb.jhu.edu/software/centrifuge/]
cutadapt 1.14 Quality and adapter trimmer for sequencing reads [https://github.com/marcelm/cutadapt]
diamond 0.9.10 Accelerated BLAST-type searching for protein sequences [https://github.com/bbuchfink/diamond]
fastqc 0.11.5 Venerable sequencing quality analysis software [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/]
mothur 1.39.5_2 Community analysis using marker genes [https://mothur.org/]
pilon 1.22 Assembly polishing using Illumina reads [https://github.com/broadinstitute/pilon]
poretools 0.6.0_6 Tools for working with nanopore data [https://github.com/arq5x/poretools]
racon 0.5.0 Assembler for long, uncorrected reads [https://github.com/isovic/racon]
snp-dists 0.2 Quickly calculate SNP distances between aligned sequences [https://github.com/tseemann/snp-dists]
trim-galore 0.4.4 Wrapper for cutadapt. Automatically determines adapter type [https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/]
unicycler 0.4.1 Hybrid assembler for long- and short-read data. Automated assembly polishing. Also does short-read-only assemblies [https://github.com/rrwick/Unicycler]
velvetoptimiser 2.2.5 Optimises velvet assembly options [https://github.com/tseemann/VelvetOptimiser]

Updated tools

abricate 0.4 0.7 Updated to include NCBI’s resistance database. Handles more assembly formats. [https://github.com/tseemann/abricate/releases]
andi 0.10_1 0.11 Minor updates [https://github.com/EvolBioInf/andi/releases]
artemis 16.0.11 16.0.17 Switch NCBI BLAST to HTTPS [https://github.com/sanger-pathogens/Artemis/releases]
bowtie 1.2.0 Bugfix [https://github.com/BenLangmead/bowtie/releases]
bowtie2 2.3.0 2.3.3 Static linking of compression and threading libraries to improve portability [https://github.com/BenLangmead/bowtie2/releases]
bwa 0.7.15 0.7.16a Bugfix [https://github.com/lh3/bwa/releases]
canu 1.5 1.6 Stable, tested and documented (https://canu.readthedocs.org/) release [https://github.com/marbl/canu/releases]
cd-hit 4.6.6 4.6.8 Now works with paired-end reads [https://github.com/weizhongli/cdhit/releases]
fasttree 2.1.8 2.1.10 Bugfix [http://www.microbesonline.org/fasttree/ChangeLog]
figtree 1.4.2 1.4.3 Bugfix [http://tree.bio.ed.ac.uk/software/figtree/]
freebayes 1.1.0 1.1.0_1 Brew packaging fix to solve problems with freebayes-parallel
genometools 1.5.9 1.5.10 Bugfix [https://github.com/genometools/genometools/releases]
gubbins 2.2.0_1 2.3.1 Now outputs tree with internal nodes labelled [https://github.com/sanger-pathogens/gubbins/releases]
mash 1.1.1_1 2 New command “screen” to estimate “containment within” rather than “distance to” a read set [https://github.com/marbl/Mash/releases]
nanopolish 0.5.0_1 0.7.2 Loads of fixes [https://github.com/jts/nanopolish/releases]
nullarbor HEAD-d938d30 HEAD-1495981 Experimental nullarbor2 – probably unstable! [https://github.com/tseemann/nullarbor/commit/1495981d6cba1136265bd4c85460c4768d464710]
prodigal 2.6.2 2.6.3 Bugfix [https://github.com/hyattpd/Prodigal/releases]
python 2.7.13 2.7.14 Version update
python3 3.6.1 3.6.3 Version update
samtools 1.4 1.5 Samtools fastq can now make gzipped fastqs [https://github.com/samtools/samtools/releases]
spades 3.10.1 3.11.0 Performance improvements [http://spades.bioinf.spbau.ru/changelog.html]
vsearch 2.4.3 2.4.4 Bugfix and documentation improvement [https://github.com/torognes/vsearch/releases]

New GVL instances will receive these updates automatically. You can pull in these updates into an existing GVL instance by running brew update && brew upgrade.