Recent Releases of ariba
ariba - Version 2.14.7
See CHANGELOG for details.
- Python
Published by Oliver-Lorenz-dev over 2 years ago
ariba - Version 2.14.0
- New feature to download NCBI Antimicrobial Resistance Gene Database, provided by schultzm
- Bug fix to fermilite path provided by schultzm
- Updates to the Docker file including update of Ubuntu version
- A SIGPIPE handling code change
- Required Python 3 version increased to 3.6
- matplotlib version increased to >=3.1.0
- Documentation updates
- Python
Published by kpepper over 6 years ago
ariba - Version 2.13.4
Added fix for GitHub issue #255.
- Python
Published by kpepper almost 7 years ago
ariba - Version 2.13.3
Small change to TB panel (gyrA D94A -> ciprofloxacin resistance)
- Python
Published by martinghunt about 7 years ago
ariba - Version 2.13.2
Update TB variant panel to match mykrobe's.
- Python
Published by martinghunt about 7 years ago
ariba - Version 2.13.1
Bug fix from previous release, which had missing data directory.
- Python
Published by martinghunt over 7 years ago
ariba - Version 2.13.0
This release is broken. Use 2.13.1 instead.
- fix missing linebreaks in resfinder download (issue #236)
- added experimental Mycobacterium tuberculosis AMR calling using built-in panel of variants.
- Python
Published by martinghunt over 7 years ago
ariba - Version 2.12.1
Bug fix: getref virulence finder was incorrectly getting plasmidfinder (issue #216)
- Python
Published by martinghunt over 7 years ago
ariba - Version 2.12.0
- stop spades warnings (issue #214)
- get latest plasmidfiner, resfinder, virulencefinder data from bitbucket (issues #216, #218)
- update srst2_argannot to version r2 (issue #217)
- Python
Published by martinghunt almost 8 years ago
ariba - Option to use SPAdes and multithreading for Bowtie2 and SPAdes
Enhancements from @andreyto
- Python
Published by andrewjpage about 8 years ago
ariba - Version 2.10.3
Bug fix: the 'hetmin' column of the MLST detailed report was getting the max instead of min.
- Python
Published by martinghunt over 8 years ago
ariba - Version 2.10.2
Fixes CARD downloads issue #200 - thanks @JezSw.
- Python
Published by martinghunt over 8 years ago
ariba - Version 2.10.1
Fix read mapping behaviour for bowtie2 version >2.3.1. Addresses issue #190.
- Python
Published by martinghunt over 8 years ago
ariba - Version 2.10.0
Addresses issues raised by reviewers:
- new task "expandflag" that expands each flag number in the report.tsv file into a breakdown of its meaning
- y-axis label in plot made by micplot fixed (it should not have said "log")
- for complete genes, all variants are reported. Previously, anything after the first frameshift was filtered out of report.tsv (but everything is still in debug.report.tsv)
- prepareref writes warnings to stderr if any genes or variants are removed, directing the user to the log files for more information.
- Python
Published by martinghunt over 8 years ago
ariba - Version 2.9.4
Bug fix getting card version 1.1.8 (issue #178).
- Python
Published by martinghunt almost 9 years ago
ariba - Version 2.9.3
Bug fix for names for pubmlst scheme for "Acinetobacter baumannii#1". Everything was "ND".
- Python
Published by martinghunt almost 9 years ago
ariba - Version 2.9.2
Tweak to Bowtie2 options for Bowtie2 version 2.3.1, so it's consistent with Bowtie2 versions <2.3.1 (issue #170).
- Python
Published by martinghunt almost 9 years ago
ariba - Version 2.9.1
- bug fix in summary (key error KeyError: 'yesmultihet')
- removed debugging print statements (issue #172)
- Python
Published by martinghunt almost 9 years ago
ariba - Version 2.9.0
- add VirulenceFinder to getref (issue #165)
- add new column to summary: ctg_cov
- Python
Published by martinghunt almost 9 years ago
ariba - Version 2.8.1
- new task micplot
- bug fix where sometimes erroneous variants called if position in ref matched same contig in two different places
- Python
Published by martinghunt almost 9 years ago
ariba - Version 2.7.2
Fixes issue #157. Now requires pymummer >= 0.10.2.
- Python
Published by martinghunt about 9 years ago
ariba - Version 2.7.1
Bug fix writing Newick tree for Phandago when using Dendropy 4.2.0. Bug fixed, but now ariba requires dendropy >= 4.2.0 instead of previous 4.1.0.
- Python
Published by martinghunt about 9 years ago
ariba - Version 2.7.0
Added support for megares. https://megares.meglab.org/
- Python
Published by martinghunt about 9 years ago
ariba - Version 2.6.1
Bug fix reading some mlst files (should ignore more columns)
- Python
Published by martinghunt about 9 years ago
ariba - Version 2.6.0
- add support for MLST and getting schemes from pubmlst
- improve het snp calls by checking for strand bias
- Python
Published by martinghunt about 9 years ago
ariba - Version 2.5.1
Fix rare edge case where best assembly was not always being chosen, resulting in apparent truncated assemblies.
- Python
Published by martinghunt about 9 years ago
ariba - Version 2.5.0
Bug fixes: - better choosing of closest reference sequnce - minimap was not reporting hits for large clusters, so missing from final output - some variants were being missed, and in the case of indels causing errors. Fixed by not using -C option of show-snps
- Python
Published by martinghunt over 9 years ago
ariba - Version 2.4.0
- improved how closest ref seq is chosen
- Mash no longer a dependency
- expose --threads option (but it is still experimental)
- "yes" and "yes_nonunique" now have same colour in phandango
- %identity column in report is now the % identity of the longest nucmer match between contig and reference (used to be mean% of all matches)
- Python
Published by martinghunt over 9 years ago
ariba - Version 2.3.0
- not backwards compatible. Files made by prepareref, and the report.tsv have changed.
- resfinder download using getref is fixed
- getref cleans up all temporary files (issue #135)
- getref has a new option --debug, which keeps all temporary files
- original sequence names are reported (issue #136)
- --force option added to the run task (issue #138)
- partial matches are reported by summary (issue #141)
- full codon change is reported in report.tsv (issue #142)
- uses $TMPDIR if it is set (issue #143)
- general improvements to reporting of samtools read depths and variant depths
- better filtering of read mapping before assembly
- extra checks to stop cases where extra copy of allele erroneously reported as partially present
- Python
Published by martinghunt over 9 years ago
ariba - Version 2.2.5
- improvements related to calling and reporting het variants
- remove dependency on samtools and bcftools
- remove unused code, was required before Mash was being used
- Python
Published by martinghunt over 9 years ago
ariba - Version 2.2.4
Bug fixes: - reference sequences are renamed more aggressively, to stop third party tools dying - various fixes involving reporting heterozygous snps
- Python
Published by martinghunt over 9 years ago
ariba - Version 2.2.3
Fixes a bug in rare cases when running ariba summary (was dying with error ariba.summaryclustervariant.Error: Mismatch in number of inferred nucleotides ...)
- Python
Published by martinghunt over 9 years ago
ariba - Version 2.2.2
Fixes a few bugs relating to contig names and renaming. Now replaces any of the following with an underscore: | ( ) [ ] ; " ' : ! @ , -
- Python
Published by martinghunt over 9 years ago
ariba - Version 2.2.1
Fixes aln2meta that was broken from last release.
- Python
Published by martinghunt over 9 years ago
ariba - Version 2.2.0
Changes: - summary variant reporting options simplified - summary phandango colours tweaked (NAs are now white) - summary reports "interrupted" in the assembled column for full length genes that have stop codon/frameshift mutations - add SRST2's version of argannot to getref - add VFDB full to getref, so can now choose between vfdbcore and vfdbfull - add option --allcoding to preparef. Gives an alternative to suppling a metadata tsv file - add option --onlycluster to summary to pull out one cluster
Bug fixes: - can handle whitespace in FASTA headers - various small fixes in summary output (particularly for variants) - report column refbaseassembled sometimes incorrectly reported the ref length
- Python
Published by martinghunt over 9 years ago
ariba - Version 2.1.0
Changes: - report het snps for noncoding sequences - add plasmidfinder - write all assemblies to a single file at the end - better naming of clusters when using argannot
Bug fixes: - off by one error in ref and contig positions of variants in some report lines - samtools/bcftools parameters changed for snp calling. Diploid assumption was making some Q scores zero, so got filtered out when they shouldn't have - cluster naming fixed (was getting broken by vfdb) - catch when no proper pairs mapped and nothing gets assembled. Writes empty report instead of crashing.
- Python
Published by martinghunt over 9 years ago
ariba - Version 2.0.0
Significant methods, run time, and quality of results improvements over previous version. - not backwards compatible. File formats have changed - reference sequences can be noncoding or genes, and presence/absence or variants only - initial mapping to allocate reads to clusters with minimap and cd-hit-est-2d instead of bowtie2 - better cluster naming - assembly with fermi-lite instead of spades+sspace+gapfiller (assemblies are so small that sspace and gapfiller were not doing anything anyway) - find nearest reference sequences using MASH - rough tree for Phandango made using dendropy, removing the dependency on R and its ape package
- Python
Published by martinghunt over 9 years ago
ariba - Version 1.0.1
Bug fix: sometimes false-positives called, when whole gene apparently assembled, but it should not have been. Caused by using spades --untrusted-contigs option. Now --untrusted-contigs option is not used.
- Python
Published by martinghunt over 9 years ago
ariba - Version 1.0.0
Major improvements since the previous version - Not backwards compatible. File formats have changed. - Can download and use data from CARD, Resfinder, Argannot and VFDB - Better handling of variants - Support non-coding sequences in addition to genes - More readable summary files and better Phandango output - Multithreading - Numerous methods improvements and bug fixes
- Python
Published by martinghunt almost 10 years ago
ariba - Version 0.6.0
- New flag hasnonsynonymousvariants
- summary output number 3 now split into two numbers 3 or 4: 3=gene present in a unique contig that has at least one non-synonymous variant. 4=as 3, but no non-synonymous variants
- option to output all samples when running summary, ie do not remove rows/columns that are all zeros (ariba summary --no_filter)
- Python
Published by martinghunt over 10 years ago
ariba - Version 0.5.0
- Handle the case when no reads map to any of the reference genes
- Make nicely formatted fasta file of reference genes to stop tools dying
- Write fasta files of assembled gene sequences for each cluster
- bug fix: refcheck now dies if there are spaces in any sequence name
- Python
Published by martinghunt over 10 years ago
ariba - Version 0.4.1
SPAdes option changed from --trusted-contigs to --untrused-contigs, so that it doesn't output contigs that are not present in the reads
- Python
Published by martinghunt over 10 years ago
ariba - Version 0.4.0
- added an option to skip running cd-hit
- new flag for when a contig has >1 match to gene, but hits are on opposing strands
- Python
Published by martinghunt over 10 years ago
ariba - Version 0.3.2
Bug fix: sometimes there is zero read depth ina contig at a position where a variant was called by comparing contig to reference gene. This was causing ARIBA to crash.
- Python
Published by martinghunt almost 11 years ago
ariba - Version 0.3.1
Bug fixes: - stop trying to give SSPACE s.d. >1 - don't run local assembly when closest gene in cluster not found (usually becuase not enough reads in the cluster) - there was an error getting read depth at indels
- Python
Published by martinghunt almost 11 years ago
ariba - Version 0.3.0
- more columns in output
- use bowtie2 instead of smalt
- sspace/gapfiller optional
- sanity check input genes fasta
- Python
Published by martinghunt almost 11 years ago
ariba - Version 0.2.0
Cluster reads before assembling. Use closest gene from each cluster to aid local assembly.
Tidy up verbose output
Clean up output directory automatically
- Python
Published by martinghunt about 11 years ago
ariba - Version 0.1.2
Use SPAdes instead of Velvet by default. Better handling of paths to external programs.
- Python
Published by martinghunt about 11 years ago