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Achievement: Pull Sharkx3Achievement: Pair ExtraordinaireAchievement: QuickdrawAchievement: Starstruck

Achievements

Achievement: Pull Sharkx3Achievement: Pair ExtraordinaireAchievement: QuickdrawAchievement: Starstruck

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raufs/README.md

Rauf Salamzade - Grad Student @ University of Wisconsin - Madison / Kalan Lab

Interested in microbial ecology and evolution.

Scientific studies:

Peer reviewed + preprint studies I have contributed to can be found on my Google Scholar 👨‍🎓

Software developed:

🐍 = on Bioconda; 🐋 = on Docker Hub; 🥧 = on PyPi

Active development:

  • zol (& fai): 🐍 🐋 suite for evolutionary and functional analysis of gene clusters (co-located sets of genes).
  • skDER (& CiDDER): 🐍 🐋 programs for genomic dereplication using ANI and pan-genome saturation approximation.
  • lsaBGC-Pan: 🐍 🐋 suite/workflow for pan-BGC-ome analyses.
  • codoff: 🐍🥧 program to statistically assess differences in codon usage between a focal region and the background genome.

Supported but no longer in active development:

  • lsaBGC: 🐋 suite for genomic and metagenomic mining of micro-diversity in BGCs and general evolutionary analysis.
  • ConSequences: programs to find long (>10 kb) contiguous and conserved (> 99% identity) segments across genomes associated with specific geographic locations.
  • seQouia: framework for diverse omics workflows, primarily focused on QC, processing and analysis of bacterial (meta-)genomic sequencing datasets.
  • AncestralGeneRator: programs to simplify ancestral state reconstruction of ortholog group copy counts across phylogeies.
  • PerMutation: Programs for statistical determination of essential and conditionally essential genes from E. faecalis TnSeq datasets.

Pinned Loading

  1. Kalan-Lab/zol Kalan-Lab/zol Public

    zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)

    Python 48 4

  2. skDER skDER Public

    skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and metagenomics.

    Python 40 3

  3. Kalan-Lab/lsaBGC-Pan Kalan-Lab/lsaBGC-Pan Public

    lsaBGC - suite for pan-BGC-omics analysis

    Python 18 2

  4. Kalan-Lab/codoff Kalan-Lab/codoff Public

    codoff: a program to measure the irregularity of the codon usage for a single genomic region (e.g. a BGC, phage, etc.) relative to the full genome.

    Python 10 1

  5. broadinstitute/ConSequences broadinstitute/ConSequences Public

    Suite to delineate contiguous and conserved sequences from assemblies and search for their presence in raw sequencing data.

    Python 2 1

  6. broadinstitute/seQuoia broadinstitute/seQuoia Public

    A framework for diverse omics workflows, primarily focused on QC, processing and analysis of bacterial genomic sequencing sets.

    Python 2 2