Tag: BBMerge

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…

Small RNA sequencing using Illumina 2 channel SBS: how to deal with Gs? 1 I’m working on a small RNA sequencing experiment (150 PE on NovaSeq 6000), and many reads look like this when the fragment size is smaller than 150 bp, with Gs completing the sequence up to 150:…

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…

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…

Quantify the number of sequences in common paired-end sequencing data 1 Hello, I have two fastq files with the forward(Read1) and reverse(Read2) paired reads. How could I count the number of sequences in common between Read1.fastq and Read2.fastq files? (I mean, since they have the same SeqID) And, how could…

What are the definitions of the BBMerge outinsert table file? 0 I have the output from the outinsert parameter of bbmerge. I have been unable to find the explanation of the columns. Can someone explain the columns a bit more? There are status flags of I, P, or F. What…

Bond PL, Hugenholtz P, Keller J, Blackall LL. Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors. Appl Environ Microbiol. 1995;61:1910–6. Article  CAS  PubMed  PubMed Central  Google Scholar  Wang Z, Guo F, Liu L, Zhang T. Evidence of carbon fixation pathway in a bacterium from candidate…

“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…

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…

Looking for a package to detect and analyze the pairing of inline barcodes in merged reads 0 I have some fastq files with sequences which I reconstructed by merging forward and reverse reads using bbmerge. The 5′ and 3′ end of said reads must contain a 6bp inline barcode for…

Manzin, A., Mallus, F., Macera, L., Maggi, F. & Blois, S. Global impact of Torque teno virus infection in wild and domesticated animals. J. Infect. Dev. Countries 9, 562–570 (2015). Article  CAS  Google Scholar  Biagini, P. et al. Family Anelloviridae. In Virus Taxonomy: Ninth Report of the International Committee on…

Hello, I am trying to learn DNA sequencing analysis by using GIAB datasets [Link to Chinese trio – HG005_NA24631_son/], the readme file they had provided does not provide the adapter sequences used. I tried to use bbmerge.sh like in this biostars post ; bbmerge.sh in1=r1.fq in2=r2.fq outa=adapters.fa and it identified…

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…

I’ve been using BBMerge recently to address a very specific problem: I am sequencing pooled short DNA molecules (< 400bps) using paired end reads (average length ~ 230 bps post trimming) Each molecule can be assumed to be different (i.e. contains sequence differences – substitutions & indels – with respect…

Getting nucleotide frequencies per position 0 Hi, I am very new to bioinformatics and was given the task to analyze some total RNA sequencing results. So far I have converted my .fastaq files to indexed .bam using samtools index. I found the following in literature: # Generate nucleotide counts per…