Genomics and Phylogenetic Studies

A PacBio and Hi-C tomato genome rebuild shrinks gaps from 81.71Mb to 44Kb; the matching ITAG4.0 annotation adds 4,794 genes and updates most carried-over models.

A convolutional network trained on 16S reads from 13,838 species reaches within 2.0% of training-set Bayes-optimal species accuracy and usually beats k-mer, alignment and Kraken2 on held-out-species genera.

Building the repeat graph from fast, possibly misassembled contigs lets Flye resolve repeats and produce more contiguous long-read assemblies, with fewer errors than Canu on human and worm genomes.

fastq-pair, a C tool, re-pairs paired-end fastq files by hashing read identifiers and file offsets, writing matched pairs plus singleton files with linear time and memory scaling.

decontam, an R package, classifies contaminant sequences in marker-gene and metagenomic data by their inverse frequency-DNA concentration relationship and higher prevalence in negative controls.

FastANI accurately estimates average nucleotide identity (ANI) up to 782-fold faster than BLAST; across 90K prokaryotic genomes, an 83-95% ANI gap supports a 95% species boundary.

Split k-mer matching lets SKA cluster and align related bacterial genomes from raw reads, matching a mapping pipeline's MRSA outbreak tree topology with nearly 17 times less CPU time.

Per-sample assembly with gVCF output, followed by joint genotyping, lets GATK HaplotypeCaller scale linearly with cohort size while calling indels more accurately than SAMtools, UnifiedGenotyper or Platypus.

fastp unifies FASTQ quality control, adapter trimming, filtering, and base correction in one scan; single-threaded, it ran 2–5 times faster than FASTQC, Cutadapt, or Trimmomatic.

GLnexus, a joint variant caller backed by an incrementally growable gVCF database, largely matched GATK on 50,000 exomes while keeping more rare indels and using 3.8–6.6-fold fewer core-hours.

NanoPack bundles Python3 tools (command line, GUI, web service) for QC plotting, summary statistics, read filtering and contaminant removal of Oxford Nanopore and PacBio long reads.

Nanopore-only sequencing of GM12878 across 39 MinION flowcells (91.2 Gb) yielded an assembly with NG50 ∼3 Mb; adding 5× ultra-long reads raised NG50 to 6.4 Mbp.

BUSCO v3 quantifies genome, gene set and transcriptome completeness via near-universal single-copy orthologs and repurposes them for gene predictor training, reference selection, and phylogenomic marker discovery.

dRep groups genomes with fast Mash distances, then accurate ANI, de-replicating 1,125 infant gut genomes in 92 CPU hours versus 2,784 for naive gANI.

Read pairs that fail kallisto pseudoalignment because of conflicting matches are filtered by pizzly to call, assemble and quantify gene fusions from raw RNA-seq in minutes rather than hours.

Unicycler scaffolds SPAdes short-read assembly graphs using long reads, producing more complete bacterial assemblies with fewer misassemblies than competing hybrid tools, even at low long-read depth.

Sentieon's rewrite of GATK and MuTect pipelines runs on average 36x faster than GATK Best Practices on public human data while matching its calls (average F-score 0.9996).

BugBase assigns pathway coverage and traits (Gram stain, oxygen tolerance, pathogenicity) to individual taxa in 16S or shotgun microbiome data, detecting some functional differences bag-of-genes profiles miss.

Canu's tf-idf weighted MinHash overlapping and error-filtered sparse overlap graph yield complete Nanopore microbial genomes and contig NG50 above 21 Mbp for PacBio human and Drosophila.

Filtering STAR's chimeric alignments against gene annotations outscored 15 other fusion callers on 60 cancer cell lines and ran fastest, averaging 2.3 single-core hours per sample.

Re-aligning reads to both alleles gives WhatsHap the lowest PacBio switch error rates (full coverage: 0.24% real, 0.02% simulated) and better indel phasing than hapCUT and phASER.

Quality-score-free UNOISE2 clusters unique Illumina amplicon reads by abundance skew and edit distance with two preset parameters, matching or exceeding DADA2 accuracy on 16S mock communities.