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Charting a Future for Sequencing RNA and Its Modifications A New Era for Biology and Medicine (2024) / Chapter Skim
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Appendix A: Tables of Computational Tools
Pages 177-179

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From page 177...
... SACall Convolution layers, FAST5 fasta/fastq https://github.com/huangnengCSU/SACall transformer self-attention basecaller layers and a CTC decoder CATCaller convolution-augmented FAST5 fasta/fastq https://github.com/biomed-AI/CATCaller transformer architecture Halcyon CNN module and RNN- FAST5 fasta https://github.com/relastle/halcyon based encoder and decoder continued Prepublication Copy 177
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From page 178...
... NanoPack Long-read QC tool written in FASTQ, sorted bam, HTML, PDF, https://github.com/wdecoster/nanopack python language & sequencing PNG, & JPG summary files ToulligQC QC tool for guppy basecalled sequencing HTML https://github.com/GenomicParisCentr files, written in python3. summary files e/toulligQC MinIONQC Non-interactive tool written in Sequencing PNG & YAML https://github.com/roblanf/minion_qc R
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From page 179...
... Flye Repeat graphs from the analysis FASTA or FASTQ FASTA https://github.com/fenderglass/Flye of random paths in an unknown format, repeat graph, called disjointigs. uncompressed or compressed with gz Shasta Run-length representation of the FASTA/FASTQ FASTA/GFA https://github.com/chanzuckerberg/ read sequence.
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Key Terms

  • tool written
  • summary file
  • fastq fasta
  • summary files
  • bruijin graph

  • index file
  • jpg summary
  • extension step
  • architecture halcyon
  • decoder catcaller

  • nor summary
  • guppy basecalled
  • analysis fasta
  • python language
  • web application

  • file boardion
  • fuzzy bruijin
  • source hisat
  • repeat graphs
  • pacbio bam

  • format pycoqc
  • pdf report
  • application based
  • ctc decoder
  • reference genome

  • single reference
  • seed extension
  • cnn module
  • sorted bam
  • transformer architecture


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