Tag: BBTools

Potent latency reversal by Tat RNA-containing nanoparticle enables multi-omic analysis of the HIV-1 reservoir

Participants and blood collection A total of n = 23 HIV-1 seropositive individuals on stably suppressive ART were included in this study (Supplementary Table 1). Participants were recruited at Ghent University Hospital. 2/23 individuals are female, 21/23 are male; the limited representation of female individuals in our study is a direct reflection of…

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Merge overlapping paired end reads from BAM file.

Merge overlapping paired end reads from BAM file. 0 Hi everyone, Using Trimmomatic and then HISAT2, I have aligned 300 RNA fastq samples (NovaSeq6000, RNA sequencing, paired-end, 150bp sequencing). I have found a percentage of overlapping paired end reads (read through) in the 300 .bam files. I found the overlaps…

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MetaSPAdes genome assembly (shotgun metagenome singleend) – usegalaxy.org support

Busrak December 11, 2023, 3:31pm 1 Hi friends, Metagenomic single end raw data with cut adapt‘Maximum error rate 0.3’Match times: 1Minimum overlap length:3minimum lenght: 15Max N: 0.3Max expected errors: 30 parameters.Then I aligned the host genome with gallus gallus with BBmap tool. I want to Assembly unmapped read. However, MetaSPAdes…

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Building reference dbSNP file using WGS samples

Building reference dbSNP file using WGS samples 2 Dear scientific community, I have to call variants from WGS samples of citrus. I used GATK pipeline for post processing of aligned reads but reference dbSNP file is not available for citrus sinensis. I am using bootstraping method. Removed duplicates and called…

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Debian — Details of source package bbmap in bookworm

Links for bbmap Debian Resources: Maintainers: External Resources: The following binary packages are built from this source package: bbmap BBTools genomic aligner and other tools for short sequences bbmap-jni short read aligner and other bioinformatic tools – JNI library Other Packages Related to bbmap adep: debhelper-compat (= 13) Package not…

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Yes .. BBMap can do that!

NOTE: This collection was originally posted at SeqAnswers.com. Creating a copy here to preserve the information.Part I is available here: Yes .. BBMap can do that! – Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)Part II is available here: Yes .. BBMap can…

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BBtools bug in reporting the number of substitutions in the console output, it seems to report insanely high rates of heterozygosity

Hello, I know Brian is sometimes around, but here is my command: while read p; do callvariants.sh in=${p}.recal.bam ploidy=2 vcf=${p}.20score.vcf useidentity=f overwrite=true ref=ref.fsa -Xmx50g ; done <ID java -ea -Xmx50g -Xms50g -cp /home/alessandro/software/bbmap/current/ var2.CallVariants in=ancestor.recal.bam ploidy=2 vcf=ancestor.20score.vcf useidentity=f overwrite=true ref=ref.fsa -Xmx50g Executing var2.CallVariants [in=ancestor.recal.bam, ploidy=2, vcf=ancestor.20score.vcf, useiden tity=f, overwrite=true, ref=Adineta_vaga.fsa,…

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How to get unaligned reads and aligned reads into separate files from SAM/BAM?

How to get unaligned reads and aligned reads into separate files from SAM/BAM? 0 I have long reads aligned with MiniMap2 in the form of SAM file. I want to get my unmapped reads into a file called unmapped.fastq.gz and my aligned reads into a file called mapped.fastq.gz. How can…

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Shorten Illumina reads

Shorten Illumina reads 1 I have a somewhat unusual question: I want to change the paired-end read size from 150 bases to 101 bases for the entire library. I am working with RepeatExplorer2 in protocol-2 (Comparative analysis) mode, and it requires the same read length for all libraries. However, one…

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Bbtools callvariant multisample mode, + base recalibration

Bbtools callvariant multisample mode, + base recalibration 0 Hello, it’s not clear to me if the multisample mode is actually a join calling, or if it’s simply the equivalent of bcftools norm + bcftools merge. I am specifically interested in NOT doing join calling. I am also wondering if base…

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The metagenomic and metabolomic profile of the gut microbes in Chinese full-term and late preterm infants treated with Clostridium butyricum

Ethics approval and consent to participate The study was approved by the Human Research Ethics Committees of the Children’s Hospital of Soochow University (Reference 2020CS017). All specimens were collected according to the guidelines set by the Children’s Hospital of Soochow University. All authors confirm that all methods were performed in…

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Viral positive and negative strand with paired sequencing and bowtie

You should expect the same number of forward and reverse strand reads because read 1 and read 2 are on opposite strands. What would be more interesting here is to first split the mapped file into r1 and r2, then split THOSE files into forward and reverse, then combine R1…

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Detect STRs in illumina library

Detect STRs in illumina library 1 I have paired-end whole genome sequencing data, and I would like to try finding STRs (Short Tandem Repeats) in this data. What tools should I use? There is no assembled reference genome available for my species. repeats annotation STR • 272 views BBMask in…

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Aligner with statistics included?

Aligner with statistics included? 1 Hello, Is there a long range aligner that could make a statistics outlook listing how many SNP, indels etc are observed in the alignment itself? Thank you aligner alignment • 203 views BBTools’ callvariants.sh calls variants only from the alignments. So: callvariants.sh in=nxyxx.bam ref=ref.fa yields:…

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checkstrand tool (from BBMap suite) question

checkstrand tool (from BBMap suite) question 0 Brian Bushnell : I was looking at checkstrand.sh application included in the latest version of BBMap. While running a test analysis using a human sample I noticed that the output for the tool was identical in following two scenarios using a single end…

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BBTools 39.03 released!

Hi Everyone, I just released a new version of BBTools (39.03). There are some exciting new features like neural networks. But let me list them: 1) New program called “bbcrisprfinder.sh”. It finds CRISPRs… designed for short reads in metagenomes (but it’s also OK on full genomes). It works better if…

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BBTools 39.03 releaed!

Hi Everyone, I just released a new version of BBTools (39.03). There are some exciting new features like neural networks. But let me list them: 1) New program called “bbcrisprfinder.sh”. It finds CRISPRs… designed for short reads in metagenomes (but it’s also OK on full genomes). It works better if…

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Oxygen respiration and polysaccharide degradation by a sulfate-reducing acidobacterium

Rabus, R., Hansen, T. A. & Widdel, F. In Dissimilatory Sulfate-and Sulfur-Reducing Prokaryotes. The Prokaryotes: Prokaryotic Physiology and Biochemistry, Rosenberg E., DeLong E. F., Lory S., Stackebrandt E., and Thompson F. at (2013). Rabus, R. et al. Chapter Two—A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing…

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MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data

Real metaHi-C datasets In this study, we leveraged several publicly available metagenomic Hi-C datasets, consisting of two short-read metaHi-C datasets and two long-read metaHi-C datasets. The specific sizes of raw datasets were shown in Supplementary Table 6. Two short-read metaHi-C datasets were generated from different microbial ecosystems, including human gut (BioProject:…

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How to subset large BAM files specifically/ extract specific subsets?

Dear community, I have huge BAM files (mapped using BBTools+coordinate-sorted via SAMTOOLS), which I used for variant calling. Now I would like to manually check specific positions/ variants in the mapped data using Tablet and/or IGV. Unfortunately, the BAM files are extremely large, rendering it impossible to download them from…

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Integrating chromatin conformation information in a self-supervised learning model improves metagenome binning [PeerJ]

Introduction The rapid proliferation of high-throughput sequencing in metagenomics, combined with the advancement of scalable computational tools, has allowed scientists to digitally isolate tens of thousands of microbial genomes from large collections of metagenomic datasets (Nayfach et al., 2021). Although these genomes are only the tip of the iceberg of…

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A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil

Field sample collection Topsoil samples (0–15 cm, roughly 0.5 m3) from replicate field plots were collected from the Hopland Research and Extension Center (HREC) in Northern California, which is unceded land of the Shóqowa and Hopland People, on August 28th, 2018 after experiencing mean annual precipitation during the rainy season, see our…

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Phage-microbe dynamics after sterile faecal filtrate transplantation in individuals with metabolic syndrome: a double-blind, randomised, placebo-controlled clinical trial assessing efficacy and safety

Study design We set up a prospective, double-blinded, randomised, placebo-controlled intervention study that was performed in our academic hospital, the Amsterdam University Medical Centres location AMC in the Netherlands. After passing screening, 24 subjects with MetSyn were randomised to receive a sterile FFT from a lean healthy donor or a…

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Contrasting whole-genome and reduced representation sequencing for population demographic and adaptive inference: an alpine mammal case study

Aguirre-Liguori JA, Ramírez-Barahona S, Gaut BS (2021) The evolutionary genomics of species’ responses to climate change. Nat Ecol Evol 5:1350–1360. doi.org/10.1038/s41559-021-01526-9 Article  PubMed  Google Scholar  Andrews KR, Good JM, Miller MR, Luikart G, Hohenlohe PA (2016) Harnessing the power of RADseq for ecological and evolutionary genomics. Nat Rev Genet 17:81–92….

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BBTOOLS( bbtools ) info, BBTOOLS( bbtools ) chart, market cap, and price

BBTOOLS Cost Would like to know the latest BBTOOLS price? Here is it as well as other useful data about this kind of cryptocurrency. At TheBitTimes.Com, we collect and provide any valuable content on it such as 1 bbtools to USD so that you could make a favorable investment and…

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bbtools.eth | Address 0xa15869d1a77f2c02816bdd790d45718df9577b1f | Etherscan

” data-bs-custom-class=”popover-preview”> 0x159c17002d59e8b7513d28910c28f6ccbfc077148a85539e40774d6a718309fd Manual Swap 17743081 2023-07-21 17:43:35 1 hr 31 mins ago 1689961415 bbtools.eth OUT 0xbD1b10…96591FBD 0 ETH 0.00612944 40.29164342 ” data-bs-custom-class=”popover-preview”> 0xad5be3731f276b571633d06f44d22b915eb1d1834c3de43f24b96f7dda79d32a Transfer 17739082 2023-07-21 4:17:11 14 hrs 57 mins ago 1689913031 bbtools.eth OUT 0xbD1b10…96591FBD 0 ETH 0.00074844 15.92088759 ” data-bs-custom-class=”popover-preview”> 0xbc4300a2eaa4e1f0ea5fec4916ef594b97b006a8df26348233d0e9f18edc03fc Execute 17739079 2023-07-21 4:16:35 14 hrs…

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BuyBack Tools price – BBTOOLS to USD price chart & market cap

What is the price of BuyBack Tools today? One BuyBack Tools coin can currently be purchased for approximately $0.00002054. What is the BuyBack Tools Market Cap today? BuyBack Tools Market Cap is $20,146.13 today. What’s the last 24h BuyBack Tools trading volume? Trading volume of BuyBack Tools in the last…

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BuyBack Tools (BBTOOLS) Token Tracker

/** *Submitted for verification at Etherscan.io on 2023-07-20 */ // SPDX-License-Identifier: MIT /** BuyBack Tools 🛠 $BBTOOLS Ultimate Toolbox for transparent project spending Telegram Portal: t.me/BuyBackToolsPortal&#13; Website: www.BuyBackTools.tech&#13; Twitter: twitter.com/BBTOOLS_ETH&#13; **/ pragma solidity 0.8.20; abstract contract Context { function _msgSender()…

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Herbarium specimen sequencing allows precise dating of Xanthomonas citri pv. citri diversification history

Dark, P. & Gent, H. Pests and diseases of prehistoric crops: a yield ‘honeymoon’ for early grain crops in Europe? Oxford J. Archaeol. 20, 59–78 (2001). Article  Google Scholar  Mira, A., Pushker, R. & Rodriguez-Valera, F. The Neolithic revolution of bacterial genomes. Trends Microbiol. 14, 200–206 (2006). Article  CAS  PubMed …

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BBtools specify java temp dir (or other java options)

BBtools specify java temp dir (or other java options) 0 Is it possible to provide other java options (e.g.) -Djava.io.tmpdir to bbtools? As far as I can see, only -Xmx works. bbtools • 22 views • link updated 30 minutes ago by GenoMax 131k • written 45 minutes ago by…

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bbmap split paired-end reads back into separated fastq files?

bbmap split paired-end reads back into separated fastq files? 1 Hi, I am trying to remove human reads from my metagenomic sequences (skin samples). I have used the command recommended in the bbmap documentation: bbmap.sh minid=0.95 maxindel=3 bwr=0.16 bw=12 quickmatch fast minhits=2 path=/path/to/hg19masked/ qtrim=rl trimq=10 untrim -ea -Xmx100g in=reads.fq outu=clean.fq…

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BBDuk Guide – DOE Joint Genome Institute

“Duk” stands to Decontamination Using Kmers. BBDuk was made to combine many common data-quality-related trimming, filtering, and masking actions into an single high-performance tool. It are capable of quality-trimming or filtering, adapter-trimming, contaminant-filtering via kmer matching, sequence masking, GC-filtering, length filtering, entropy-filtering, format conversion, histogram generation, subsampling, quality-score recalibration, kmer…

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Use bbmap reformat.sh to convert from paired fq files to a bam file

Use bbmap reformat.sh to convert from paired fq files to a bam file 1 As outlined here I was able to create paired-end fastq files with the help of GenoMax . Now I wonder how I can use reformat.sh from bbmap to convert this files to a valid bam file…

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Use bbmap reformat.sh to convert from paired fq files to a valid abam file

Use bbmap reformat.sh to convert from paired fq files to a valid abam file 1 As outlined here I was able to create paired-end fastq files with the help of GenoMax . Now I wonder how I can use reformat.sh from bbmap to convert this files to a valid bam…

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Genomic screening of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential

Sample collection Sampling kits were sent out to various bat rehabilitators in the UK, as described previously56, for the collection of faeces from bats. These faecal samples (0.02–1 g) were immediately stored in 5 ml of RNAlater solution to prevent degradation of RNA. The geographical locations and collection dates for all samples…

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RCAC – Knowledge Base: Biocontainers: bbtools

bbtools Link to section ‘Introduction’ of ‘bbtools’ Introduction BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data. Docker hub: hub.docker.com/r/staphb/bbtoolsHome page: jgi.doe.gov/data-and-tools/software-tools/bbtools/ Link to section ‘Versions’ of ‘bbtools’ Versions 39.00 Link to section ‘Commands’ of ‘bbtools’ Commands Xcalcmem.sh a_sample_mt.sh addadapters.sh addssu.sh…

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bbduk.sh trimmer with multiple input files

bbduk.sh trimmer with multiple input files 0 Hi all, I am using bbduk.sh and was wondering if there’s an efficient way to process multiple sets of reads with it? E.g. if you have read 1 as 4 separate files and read 2 as 4 separate files, typical mappers like bowtie2…

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BBtools callvariants.sh

BBtools callvariants.sh 0 Hello, I am facing an interesting case, where bbtools callvariant fail to call SNPs in high density regions. I have some nanopore reads, and Clair3 telling me those regions do exist, as exemplified in the pic hereafter. I would like to tweak the callvariant to be able…

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Iterative normalization for large files using BBnorm

Iterative normalization for large files using BBnorm 1 hi all, I’m a big fan of the BBTools suite, but I’m checking that I’m not doing anything silly here. I have several terabytes of decontaminated, QC’d, error corrected reads that I’d like to normalize prior to cross assembly on the agglomerated…

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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…

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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…

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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…

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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…

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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…

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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,…

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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…

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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…

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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…

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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…

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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…

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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….

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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…

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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…

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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…

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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…

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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…

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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…

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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…

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