AWS CLI update 2.15.29 is now available.
BCFtools 1.20 includes a new short option -W for --write-index that accepts an optional parameter for choosing between TBI and CSI index formats, a new --regions-overlap option in bcftools consensus that take into account overlapping deletions that start out of the fasta file target region, a new bcftools isec option -l, --file-list to read the list of file names from a file, a --force-single option in bcftools merge to support single-file edge case, a --indels-cns option in bcftools mpileup for an alternative indel calling model, an update to bcftools norm to change the order of atomization and multiallelic splitting (when both -a,-m are given) to "split first, then atomize," an update to bcftools reheader to allow reading the input file from a stream with --fai, support for custom genotypes based on the allele with higher depth in bcftools +setGT, several updates to bcftools +split-vep, a fix to bcftools stats, new support for converting from tags using localized alleles to the family of standard tags in bcftools +tag2tag, and bcftools +trio-dnm2 to extend --strictly-novel to exclude cases where the non-Mendelian allele is the reference allele.
breseq 0.38.3 fixes a problem adding --isescan-results with Genbank input to breseq CONVERT-REFERENCE, creates output directories if they don't already exist when using the commands breseq BAM2ALN and breseq BAM2COV, allows for plus (+) and minus (−) signs for reference seq ids, and updates the syntax for the experimental breseq SOFT-CLIPPING command to allow multiple BAM inputs.
checkMySequence 20240312 is new to SBGrid. checkMySequence is used for sequence assignment validation in cryo-EM models.
cryoCARE is now at version 0.3.0.
cryoDRGN 3.1.0-beta is available as a version override. New features in this version include a new tool for removing extraneous output files from completed experiments (cryodrgn_utils clean), an update to backproject_voxel to produce half-maps and a half-map FSC by default, an option to use cryodrgn_utils fsc from the fsc analysis script for calculating Fourier shell correlations between two .mrc volume files and also plot_fsc based on plotfsc, and an update to use reparametrization in Angstroms when creating cryodrgn_utils gen_mask based on cryoem_tools.gen_mask.py.
CryoSieve 1.2.5 adds the new programs cryosieve-csrefine and cryosieve-csrhbfactor, introduces a simplified command for preparing the Conda environment, and adds support for CUDA 11.8.
DeepChem 2.8.0 is a new title. DeepChem aims to provide a high quality open-source toolchain that democratizes the use of deep-learning in drug discovery, materials science, quantum chemistry, and biology.
doubleHelix is also new at version 20240312. doubleHelix is a tool for nucleic acid sequence identification, assignment, and validation for cryo-EM and crystal structure models.
Dynamo2Relion 1.0.0 is new to the collection per user request. Dynamo2Relion converts dynamo tables to star files for RELION 4.0.
EMRNA 1.4 was added per user request. EMRNA is for deep learning based automated RNA modeling from cryo-EM maps.
EternaFold 1.3.1 is also new to the collection. EternaFold performs RNA secondary structure prediction.
Evo 0.1.1 is another new title. Evo is a program for DNA foundation modeling from molecular to genome scale.
Foldseek 8-ef4e960 add support for clustered, protein-complex searches (alpha-verison, feedback welcome) as well as improved HTML output.
Ghostscript was updated to version 10.03.0
Infernal is now at version 1.1.5. New in this version is support for M1 Macs, a default setting of 4 cores for multithreaded programs, support for building models from aligned fragmentary sequences in `cmbuild', new parallelizing options in `cmcalibrate` `--split` and `--merge`, improvements to the `--anytrunc` option to `cmscan` and `cmsearch` to return more hits that extend to the 5' and 3' ends of sequences, a new `--consrf` option to `cmbuild` for use in combination with the `--hand` option to define the RF annotation as the consensus sequence for the model, and a new tabular hits table output format for `cmscan` and `cmsearch` with the `--tblout --fmt 3` option.
LightDock 0.9.4 is the new default. This title was bumped a few versions with a number of new features. See the release notes for full details.
NGLview 3.1.2 is new to SBGrid as well. NGLview is an IPython/Jupyter widget to interactively view molecular structures and trajectories.
Phenix 1.21.1 is the new default and adds support for joint X-ray/neutron refinement to the phenix.refine GUI, fixes a DMSO restraint and excessive printing when processing PAE matrix files, includes a new tutorial for low resolution restraints, and introduces a new program - phenix.renumber_fab - for renumbering FAB chains using Kabat, Chothia, or Martin conventions.
QT version 5.15.13 was pushed out.
SAMtools 1.20 adds a --max-depth option to bedcov for more control over the depth limit used when calculating the pileup, a new mpileup --output-extra RLEN to display the unclipped read length, improved checking of symbolic flag names, an update to the --min-depth option to work for the Bayesian mode, an option to use the fastq -d tag:val option multiple times, a new fixmate -M option to check base modification (ML, MM, MN) tags and allow adjustments of modification data on hard-clipped records, an impovement to the split -d option to work on tags with integer values, an update to sort -n (by name) to sort primary reads before secondary / supplementary, and a new bedcov -H option to print column headers in the output.
spIsoNet 1.0_cu11.8 is another new one. spIsoNet corrects for the preferred orientation problem in cryoEM by self-supervised deep learning, by recovering missing information from well-sampled orientations in Fourier space.
Spring version 0.87.1723 for Linux is now available and includes internal upgrades to EMAN2 and Python3.
TomoNet is the last of the new software titles this month, at version beta_03 and per a user request! TomoNet offers a modern graphical user interface to carry out the entire pipeline of cryoET and subtomogram averaging to achieve high resolution.
