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Achievements

Achievement: Public SponsorAchievement: Pair Extraordinairex4Achievement: Pull Sharkx4Achievement: YOLOAchievement: QuickdrawAchievement: Mars 2020 ContributorAchievement: Arctic Code Vault ContributorAchievement: Starstruck

Achievements

Achievement: Public SponsorAchievement: Pair Extraordinairex4Achievement: Pull Sharkx4Achievement: YOLOAchievement: QuickdrawAchievement: Mars 2020 ContributorAchievement: Arctic Code Vault ContributorAchievement: Starstruck

Organizations

@conda-forge @fulcrumgenomics @bioconda @twinstrandbio @nf-core @seqwell @twinstrandbio-analytics @DetellaDx @PrimaryBio @Scantox-Group @fg-labs

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clintval/README.md

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I lead technical teams in biotech and write software for new genomics technologies. At Fulcrum Genomics you'll find me building tools and leading others in the fields of oncology, cell & gene editing, and precision medicine all while ensuring we deliver high-quality services to our clients and partners.

Featured

ProjectStackInstallWhat it does
unmux Language Install with bioconda Parse and demultiplex records, splitcode-style.
chum Language Install with bioconda Evaluate baits in a hybrid selection panel.
krak Language Install with bioconda An addicting set of Kraken-enhancing tools.
vartovcf Language Install with bioconda Stream VarDict variants into VCF v4.2.
neodisambiguate Language Install with bioconda Disambiguate reads mapped to multiple references.
bedspec Language PyPi Release An HTS-specs compliant BED toolkit.
typeline Language PyPi Release Dataclasses to delimited text, round-trip with types.

unmux

Demultiplex a dual-index paired-end run against a sample sheet, routing each read pair by its i7+i5 barcode concatenation:

❯ unmux "R1.fastq.gz" "I1.fastq.gz" "I2.fastq.gz" "R2.fastq.gz" \
  --extract "i7=1:0:8" \
  --extract "i5=2:0:8" \
  --extract "r1=0:0:end" \
  --extract "r2=3:0:end" \
  --group "samples=metadata.tsv" \
  --group "samples::match=i7+i5" \
  --template "r1" \
  --template "r2" \
  --sample-from-group "samples" \
  --out "demux/%sample.R%ordinal.fq"

chum

Score capture baits against a reference:

❯ chum score \
    --baits baits.fa \
    --targets targets.bed \
    --reference hg38.fa \
    --per-bait per-bait.tsv

krak

Bridge Kraken classifications into a BAM and filter by taxon:

❯ krak annotate \
      -i input.bam \
      -d /kraken-db \
      -a <(krak prep input.bam | kraken2 --db /kraken-db --output - -) \
  | krak filter -t 9606 -o output.bam

neodisambiguate

Disambiguate templates aligned to human and mouse references:

❯ neodisambiguate \
    --input dna00001.aligned-to-human.bam dna00001.aligned-to-mouse.bam \
    --output out/dna00001 \
    --names hg38 mm10

Elsewhere

LinkedIn Fulcrum Genomics Bioconda PyPI

Pinned Loading

  1. neodisambiguate neodisambiguate Public

    Disambiguate reads that were mapped to multiple references

    Scala 4 1

  2. fg-labs/chum fg-labs/chum Public

    Evaluate the effectiveness of baits in a hybrid selection panel

    Rust 3

  3. vartovcf vartovcf Public

    Convert variants from VarDict/VarDictJava into VCF v4.2 format

    Rust 6 1

  4. typeline typeline Public

    Write dataclasses to delimited text formats and read them back again

    Python

  5. revtag revtag Public

    Reverse (and complement) array-like SAM tags for negative facing alignments.

    Rust

  6. bedspec bedspec Public

    An HTS-specs compliant BED toolkit

    Python