13 Jul 2024
Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions
doi.org/10.1017/qpb.2021.18
#ONT #PacBio #Haplophasing #N50 #Pangenomics #ReadMapping #VariantCalling #LongReads #Genomics #Bioinformatics
ALT Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions https://doi.org/10.1017/qpb.2021.18
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22 Jun 2024
Efficient Construction and Utilization of k-Ordered FM-indexes with kISS for Ultra-Fast Read Mapping in Large Genomes. #ReadMapping #LargeGenomes #Bioinformatics
academic.oup.com/bioinformat…
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12 Dec 2023
invMap: a sensitive mapping tool for long noisy reads with inversion structural variants. #StructuralVariants #LonReads #ReadMapping #Bioinformatics
academic.oup.com/bioinformat…
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2,186
4 Jun 2023
A survey of mapping algorithms in the long-reads era. #LongReads #SequencingData #ReadMapping @GenomeBiology
genomebiology.biomedcentral.…
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3,127
1 Jun 2023
Love this tool from the readmapping wizard himself, @ChenLinxing !
Also works on difficult-to-assemble isolate jumbophages too - check it out!
1 Jun 2023
📢 Our viral genome quality improvement tool, COBRA, is finally out today. 👉
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16 May 2023
Efficient short read mapping to a pangenome that is represented by a graph of ED strings. #Pangenome #ReadMapping #Bioinformatics academic.oup.com/bioinformat…
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2,743
28 Jul 2022
A survey of mapping algorithms in the long-reads era. #ReadMapping #AlgorithmsSurvey @biorxivpreprint biorxiv.org/content/10.1101/…
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19 Jul 2022
This video about RNA-seq data preprocessing shows how to perform read alignment with the #geneXplain_platform
youtu.be/zb2qaFG1tWM
#RNASeq #FASTQ #FASTA #SAM #BAM #ReadMapping #ReadAlignment #sequencing #Phred #bowtie #tophat #subread #hisat2 #NextGenerationSequencing #NGS
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13 Feb 2022
Accelerating long-read analysis on modern CPUs. #ArchitectureOptimization #LongReads #ReadMapping #minimap2 biorxiv.org/content/10.1101/… @biorxivpreprint #Bioinformatics
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29 Apr 2021
Performance evaluation of pipelines for mapping, variant calling and interval padding, for the analysis of NGS germline panels. #NGS #ReadMapping #VariantCalling #Benchmarking
bmcbioinformatics.biomedcent… @BMCBioinfo
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31 Mar 2021
Comparison of #ReadMapping and #VariantCalling Tools for the Analysis of #Plant #NGS #Data
bit.ly/3luy8n6
#OpenScience #100DaysOfCode #BigData #DataScience #AI #WomenWhoCode #Linux #Python #coding #MachineLearning #serverless #SciComm #STEMeducation #phdchat #edu
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20 Mar 2021
Comparison of #ReadMapping and #VariantCalling Tools for the Analysis of #Plant #NGS #Data
bit.ly/3luy8n6
#OpenScience #100DaysOfCode #BigData #DataScience #AI #WomenWhoCode #Linux #Python #coding #MachineLearning #serverless #SciComm #STEMeducation #phdchat #edu
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17 Feb 2021
AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes. #ReadMapping #Liftover #ReferenceGenomes
biorxiv.org/content/10.1101/… @biorxiv_bioinfo
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18 Jan 2021
ProDerAl: Reference Position Dependent Alignment.
#ReadMapping
academic.oup.com/bioinformat… via #Bioinformatics
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6 Oct 2020
Comparison of ReadMapping and VariantCalling Tools for the Analysis of Plant #NGS Data
bit.ly/30Biop4
#DataScience #OpenScience #100DaysOfCode #BigData #AI #IoT #WomenWhoCode
#MachineLearning #serverless #Linux #Python #coding
#SciComm #STEMeducation #phdchat #retweet
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16 Sep 2020
Comparison of #ReadMapping and #VariantCalling #Tools for the Analysis of #Plant #NGS #Data
bit.ly/2FyUXoX
#OpenScience #SciComm #PubMed #WomenWhoCode #100DaysOfCode #plantsci #researchpaper #Bioinformatics #Genomics #CompBio #benchmarking #Linux #education #science
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6 Mar 2020
Everytime I have to check if it's samtools fastq -F4 or -f4 to obtain mapped reads... It just doesn't seem intuitive to me! #Bioinformatics #ReadMapping
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20 Feb 2020
Non-canonical splice sites are often neglected and considered sequencing and/or annotation artifacts, but many are bona fide splice sites. We add support through analysis of variant frequencies at splice site positions.
#readmapping #variantcalling #SNV
bit.ly/2P90Mex
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22 May 2019
Definitely one of the best alignment tools for sequencing reads of all lengths
#genomics #bioinformatics #readmapping
21 May 2019
bwa-mem2 pre-release. Identical alignments. 80% faster. github.com/bwa-mem2/bwa-mem2…
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24 Feb 2019
Just re-read @aphillippy @traingene et al’s paper on RefSeq database size and it’s impact on #metagenomics classification pipelines. Couple questions: 1/ you’re careful to limit to kmer tools. Do you see same effect with readmapping/hybrid tools, and ... (1/2)
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