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
| TOOL | VERSION | DESCRIPTION |
|---|---|---|
| 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
| TOOL | OLD VERSION | NEW VERSION | DESCRIPTION |
|---|---|---|---|
| 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 | 1.2.1.1 | 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.