Skip to content
View raufs's full-sized avatar
🧬
🧬
36 followers · 154 following

Achievements

Achievement: Pull Sharkx3Achievement: Pair ExtraordinaireAchievement: QuickdrawAchievement: Starstruck

Achievements

Achievement: Pull Sharkx3Achievement: Pair ExtraordinaireAchievement: QuickdrawAchievement: Starstruck

Block or report raufs

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.

Please don't include any personal information such as legal names or email addresses. Maximum 100 characters, markdown supported. This note will be visible to only you.
Report abuse

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

Report abuse
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 49 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