Skip to content
View clintval's full-sized avatar
164 followers · 449 following

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

Block or report clintval

Block user

Prevent this user from interacting with your repositories and sending you notifications. Learn more about blocking users.

You must be logged in to block users.

Maximum 250 characters. Please don’t include any personal information such as legal names or email addresses. Markdown is supported. This note will only be visible to you.
Report abuse

Contact GitHub support about this user’s behavior. Learn more about reporting abuse.

Report abuse
clintval/README.md

Cover

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

Project Stack Install What it does
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.

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

Pinned Loading

  1. neodisambiguate neodisambiguate Public

    Disambiguate reads that were mapped to multiple references

    Scala 4 1

  2. chum 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