gauravcodepro/miniprot-protein-annotator

from protein alignments to deep learning preparatory.

Language: Python - Size: 74.2 KB - Last synced: 21 days ago - Pushed: 21 days ago - Stars: 0 - Forks: 0

sanger-tol/treeval

Pipelines for the production of Treeval data

Language: Nextflow - Size: 54.9 MB - Last synced: about 4 hours ago - Pushed: about 4 hours ago - Stars: 17 - Forks: 2

tkchafin/FGTpartitioner

Parsimonious delimitation of large SNP datasets using the four gamete test

Language: Python - Size: 442 KB - Last synced: 7 days ago - Pushed: over 4 years ago - Stars: 6 - Forks: 0

gauravcodepro/protein-annotator

python package to analyze the protein coding regions for the genome annotation. It uses the miniprot for the alignment and gives you all the protein predicted mRNA, coding regions and other exon positions.

Language: Python - Size: 62.5 KB - Last synced: 29 days ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

gauravcodepro/coding-stitcher-pangenome

a coding sticher for genome annotations, which stitch all your coding regions coming out of the exon alignments and will produce the gene visualization for the pangenome

Language: Python - Size: 28.3 KB - Last synced: 29 days ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

gauravcodepro/intergenic-extractor

extracting all the intergenic regions from the genome annotation using the protein alignments.

Language: Python - Size: 52.7 KB - Last synced: 29 days ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

gauravcodepro/visualfreq

alignment visualization and phylogeny plotting for genome aliged regions.

Language: R - Size: 20.5 KB - Last synced: 29 days ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

gauravcodepro/genome-annotation-visualizer

a R function part to visualizae the genes coming from the genome alignment proteome annotations. This is a part of the evoseq R package

Language: R - Size: 37.1 KB - Last synced: 29 days ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

YogiOnBioinformatics/Teaching-Assistant-Computational-Genomics

Workshops, Course Schedule and Teaching Assistant Review from my time as a chosen Undergraduate Teaching Assistant for the University of Pittsburgh course, BIOSC1540 - Computational Genomics taught by Dr. Miler Lee.

Language: Shell - Size: 809 KB - Last synced: about 1 month ago - Pushed: about 5 years ago - Stars: 0 - Forks: 1

DhakadPankaj/Fly-annotation

A comparative annotation toolkit (CAT) pipeline for 304 fly genomes.

Language: Shell - Size: 32.6 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

twoXes/awesome-structural-bioinformatics

Structural Bioinformatics is awesome. Throw your textbook in the garbage, light the garbage can on fire, and blend the ashes into your cold brew almond milk latte and read this.

Language: Python - Size: 31.1 MB - Last synced: 18 days ago - Pushed: about 1 year ago - Stars: 56 - Forks: 9

mobinasri/secphase

Phasing reads with secondary alignments

Language: C - Size: 572 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 13 - Forks: 1

fmalmeida/easy_circos

easy_circos is a simple conda package that aims on rapidly and easily creating minimal circos configurations templates based on input data.

Language: Shell - Size: 360 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 6 - Forks: 2

ryought/mummer-idotplot

Generate interactive dotplot from mummer4 output using plotly

Language: Python - Size: 10.7 KB - Last synced: 7 days ago - Pushed: over 4 years ago - Stars: 25 - Forks: 5

ag-computational-bio/ReadXplorer

ReadXplorer - Visualization and Analysis of Mapped Sequences

Language: Java - Size: 88.5 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 3 - Forks: 0

wtsi-hpag/scanPAV

Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.

Language: C - Size: 6.28 MB - Last synced: 8 months ago - Pushed: over 6 years ago - Stars: 25 - Forks: 7

henryjuho/WGAbed

A package for handling whole genome alignments by Pádraic Corcoran and Henry Barton

Language: Python - Size: 95.7 KB - Last synced: 8 months ago - Pushed: over 4 years ago - Stars: 6 - Forks: 2

julienlag/samToPolyA

A utility to call polyA sites based on genome alignments in SAM format

Language: Perl - Size: 14.6 KB - Last synced: 8 months ago - Pushed: over 7 years ago - Stars: 3 - Forks: 3

koadman/libMems

a genome alignment library built around seed-and-extend algorithms for maximal exact and unique matches

Language: C++ - Size: 22.7 MB - Last synced: 10 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

nuno-agostinho/bwa-docker

Docker to run BWA for aligning sequences against a reference genome

Size: 0 Bytes - Last synced: 10 months ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

google/fast-simple-lcsk 📦

Fast and simple algorithms for computing both LCSk and LCSk+

Language: C++ - Size: 38.1 KB - Last synced: 28 days ago - Pushed: about 6 years ago - Stars: 20 - Forks: 12

PASSIONLab/BELLA

BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper

Language: C++ - Size: 136 MB - Last synced: 7 months ago - Pushed: about 2 years ago - Stars: 44 - Forks: 8

CGL-Deeplearning/alleleSelector 📦

Language: Python - Size: 255 KB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 1 - Forks: 0

hernanmd/hisat2_bovine

Scripts to index and align Bovine genome with HISAT2

Language: Shell - Size: 13.3 MB - Last synced: about 1 month ago - Pushed: about 6 years ago - Stars: 1 - Forks: 1

JerryPan2718/Microbiome-PTR

Calculate Peak-to-Trough Ratio (PTR), plot coverage graph, and perform quality control over contigs in a single pipeline integrating Glimmer3, Bowtie2, Sickle, and algorithms in R.

Language: C - Size: 39.1 MB - Last synced: over 1 year ago - Pushed: almost 5 years ago - Stars: 2 - Forks: 0

shehio/Computational-Biology

Language: Jupyter Notebook - Size: 21.6 MB - Last synced: over 1 year ago - Pushed: over 4 years ago - Stars: 5 - Forks: 1

koadman/mauveAligner

command-line interface software for genome alignment

Language: C++ - Size: 61.6 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

mslehre/MAS

Maximum Acyclic Subgraph (MAS) - Multiple Sequence Alignment (MSA) Game

Language: C++ - Size: 82.3 MB - Last synced: about 1 year ago - Pushed: almost 5 years ago - Stars: 1 - Forks: 0

AyushiSinha/FFTLab

Final project for Big Data, Small Languages, Scalable Systems course at JHU: Performs alignment between reads and a reference genome sequence using fast fourier transform

Size: 23.1 MB - Last synced: 8 months ago - Pushed: over 10 years ago - Stars: 1 - Forks: 0