Tag: BBTools
ChatGPT optimized for bioinformatics questions
Tool:ChatGPT optimized for bioinformatics questions 1 Hey everyone! I launched a new chatbot today that is bioinformatics focused! It’s trained on bioinformatics content and should help debug / ideate much faster for you than vanilla ChatGPT. Check it out here: ai.tinybio.cloud/chat Thanks! gpt • 165 views • link updated 1…
Genome assembly statistical tools
I’ll follow up what a few others have mentioned, but I like stats.sh within the BBTools package for raw assembly stats. I’ll then polish my assembly and pare it down to the targeted contigs (eg. those annotated as bacteria/viruses/your genome of interest/etc.) then I like to use quast/metaquast to evaluate…
BBduk reading fastq from S3 directly
BBduk reading fastq from S3 directly – Is it possibile? 0 Hello to all, I am not from Bioinf field but there is no issue for me running bbduk trimming command 🙂 I was wondering is it possibile to load paired fastq reads directly form S3 bucket? Even better, load…
Metagenomics-enabled reverse-genetics assembly and characterization of myotis bat morbillivirus
Ethics declaration Animal study was performed following the Guide for the Care and Use of Laboratory Animals. Animal experiment was approved by the Institutional Animal Care and Use Committee of Colorado State University (protocol number 1090) in advance and conducted in compliance with the Association for the Assessment and Accreditation…
SituSeq: an offline protocol for rapid and remote Nanopore 16S rRNA amplicon sequence analysis
For the initial test of this protocol, DNA extraction, PCR, Nanopore library preparation, Nanopore sequencing, and subsequent data analysis were conducted at sea aboard the R/V Atlantic Condor in August 2021 [26]. This investigational effort resulted in the sequencing and analysis of deep sea sediment samples within hours of their…
Genomic insights into the coupling of a Chlorella-like microeukaryote and sulfur bacteria in the chemocline of permanently stratified Lake Cadagno
Philippi M, Kitzinger K, Berg JS, Tschitschko B, Kidane AT, Littmann S, et al. Purple sulfur bacteria fix N2 via molybdenum-nitrogenase in a low molybdenum Proterozoic ocean analogue. Nat Commun. 2021;12:4774. Article CAS PubMed PubMed Central Google Scholar Xiong Y, Guilbaud R, Peacock CL, Cox RP, Canfield DE, Krom MD,…
Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota
Pruesse, E. et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35, 7188–7196 (2007). Article CAS PubMed PubMed Central Google Scholar Glöckner, J. et al. Phylogenetic diversity and metagenomics of candidate division OP3. Environ. Microbiol. 12, 1218–1229…
Sorting a STAR-output bam file with samtools leads to a significant reduction in size of the sorted bam file
I am not too familiar with the subject, neither with details of compression algorithms and nor the exact specification of the BAM format, but I think it is just a matter of more or less efficient compression. Various implementations of zlib exist and the samtools authors have run some benchmarks…
Mapping with bbmap.sh
Mapping with bbmap.sh 1 Hello everyone Todat I’m trying to do a mapping with bbmap but I have a problem because in the results I have NaN% in everything, this is normal? I’m using Ictalurus punctatus genome reference but my sample is pimelodus grosskopfii. In the picture you can see…
calctruequality in bbmap
calctruequality in bbmap 1 I’m trying to recalibrate Q scores of a NextSeq run using MiSeq contigs assembled with Tadpole. The commands I used to map the reads to the reference were as follows: bbmap.sh in=concatABC.fastq.gz outm=mapped.sam ref=./Lpe09_06TdpAssemblies/contigs09_06.fa ignorequality maxindel=100 minratio=0.4 ambig=toss qahist=qahist_raw.txt qhist=qhist_raw.txt mhist=mhist_raw.txt The command I used to…
Genomics discovery of giant fungal viruses from subsurface oceanic crustal fluids
Orcutt B, D’Angelo T, Jungbluth SP, Huber JA, Sylvan JB. Microbial life in oceanic crust. OSF Preprints, 2020; doi.org/10.31219/osf.io/2wxe6. Koonin EV. On the origin of cells and viruses: primordial virus world scenario. Ann NY Acad Sci. 2009;1178:47–64. Nigro OD, Jungbluth SP, Lin HT, Hsieh CC, Miranda JA, Schvarcz CR, et…
Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis
Data collection Metagenomic project information was collected from the MGnify metagenomic database31. Currently (September 2021), microbiome data (sequence, taxonomic, and functional information, etc.) of 325,323 environmental samples can be found in this database. Often, microbes from similar ecological communities have been studied by different groups at different times and locations….
bgzf_read_block] EOF marker is absent reformat.sh
BBMap/BBTools reformat.sh : real error or spurious message? [W::bgzf_read_block] EOF marker is absent reformat.sh 1 When subsampling paired-end .fastq.gz files using reformat.sh from BBMap/BBTools, I get this error message: [W::bgzf_read_block] EOF marker is absent reformat.sh I’ve checked the input files with gunzip -t, no error. The input files are a…
BBTools – BioGrids Consortium – Supported Software
AllHigh-Throughput SequencingGenomicsProteomicsVisualizationOther BBTools Description a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data. BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw, with autodetection of quality encoding and interleaving. Installation Use the following command to…
Any alternatives to BBMap’s clumpify.sh program to optimize gzip compression?
Any alternatives to BBMap’s clumpify.sh program to optimize gzip compression? 1 I’ve had some difficulties implementing this in pipelines because it randomly fails sometimes. Are there any other programs that can be used in its stead? fastq genomics rnaseq • 201 views • link updated 7 hours ago by GenoMax…
Secret BBMAP helper page – HRGV/Marmics_Metagenomics Wiki
#How to map to the assembled scaffolds.fasta bbmap is a powerful and highly flexible read mapper jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmap-guide/. For the upcoming analysis you are not interested in the typical mapping output but in statistics on the coverage on every scaffold, you can get them with scaffstats. We want to be specific…
Trying to trim last bp of several samples with BBduk at once
Trying to trim last bp of several samples with BBduk at once 1 Hi, I am trying to use BBduk to trim back my 151bp sequences to 150bp. I tried to create a loop for this so I could do one entire pool at the time, but I do not…
Haplotype divergence supports long-term asexuality in the oribatid mite Oppiella nova
Significance Putatively ancient asexual species pose a challenge to theory because they appear to escape the predicted negative long-term consequences of asexuality. Although long-term asexuality is difficult to demonstrate, specific signatures of haplotype divergence, called the “Meselson effect,” are regarded as strong support for long-term asexuality. Here, we provide evidence…
ENHANCED GRAVITROPISM 2 encodes a STERILE ALPHA MOTIF–containing protein that controls root growth angle in barley and wheat
Significance To date, the potential of utilizing root traits in plant breeding remains largely untapped. In this study, we cloned and characterized the ENHANCED GRAVITROPISM2 (EGT2) gene of barley that encodes a STERILE ALPHA MOTIF domain–containing protein. We demonstrated that EGT2 is a key gene of root growth…
