metagentools/GraphBin2

☯️🧬 Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs

Language: Python - Size: 78 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 27 - Forks: 1

ablab/quast

Genome assembly evaluation tool

Language: AMPL - Size: 580 MB - Last synced: 7 days ago - Pushed: 8 months ago - Stars: 367 - Forks: 73

nf-core/funcscan

(Meta-)genome screening for functional and natural product gene sequences

Language: Nextflow - Size: 12.9 MB - Last synced: about 23 hours ago - Pushed: 1 day ago - Stars: 56 - Forks: 18

COMBINE-lab/pufferfish

An efficient index for the colored, compacted, de Bruijn graph

Language: C - Size: 6.88 MB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 107 - Forks: 19

metagentools/MetaCoAG

🚦🧬 Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs

Language: Python - Size: 156 MB - Last synced: 22 days ago - Pushed: 23 days ago - Stars: 42 - Forks: 3

smaegol/PlasFlow

Software for prediction of plasmid sequences in metagenomic assemblies

Language: Python - Size: 37.7 MB - Last synced: 17 days ago - Pushed: almost 3 years ago - Stars: 89 - Forks: 27

metagentools/GraphBin

✨🧬 Refined binning of metagenomic contigs using assembly graphs

Language: Python - Size: 54.2 MB - Last synced: 25 days ago - Pushed: 25 days ago - Stars: 81 - Forks: 7

tseemann/abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

Language: Perl - Size: 15.5 MB - Last synced: 25 days ago - Pushed: 5 months ago - Stars: 329 - Forks: 85

omercelik-cs/dna-contig-generator

Language: Python - Size: 214 KB - Last synced: about 1 month ago - Pushed: over 5 years ago - Stars: 0 - Forks: 2

Gabaldonlab/redundans

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

Language: C++ - Size: 63.7 MB - Last synced: 13 days ago - Pushed: 5 months ago - Stars: 123 - Forks: 19

oschwengers/platon

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

Language: Python - Size: 37.4 MB - Last synced: 23 days ago - Pushed: 8 months ago - Stars: 98 - Forks: 15

NCBI-Codeathons/Domain_HMM_Boundaries

Refining Domain Boundaries and Performing Large Scale Parsing

Language: Jupyter Notebook - Size: 27.7 MB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 1

tobiasrausch/wally

Wally: Visualization of aligned sequencing reads and contigs

Language: C++ - Size: 6.98 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 89 - Forks: 6

morispi/CONSENT

Scalable long read self-correction and assembly polishing with multiple sequence alignment

Language: C++ - Size: 15.9 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 53 - Forks: 4

mtisza1/Cenote_Unlimited_Breadsticks

DEPRECATED: Discover divergent virus sequences, prune flanking cellular sequences, make basic report

Language: Shell - Size: 193 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 6 - Forks: 1

mansikath/whole-genome-sequencing-pipeline

A comprehensive workflow for de novo assembly of whole-genome shotgun sequencing data using Velvet, followed by BLAST searches to analyze assembled contigs.

Language: HTML - Size: 1.96 MB - Last synced: 4 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

mcveanlab/mccortex

De novo genome assembly and multisample variant calling

Language: C - Size: 9.86 MB - Last synced: 7 months ago - Pushed: about 5 years ago - Stars: 107 - Forks: 24

masikol/barapost

Toolkit for binning FASTA, FASTQ and FAST5 files according to taxonomic annotation

Language: Python - Size: 3.37 MB - Last synced: 7 months ago - Pushed: 12 months ago - Stars: 4 - Forks: 1

haradama/PlasmidPicker

Software to identify plasmid sequence data from metagenome using logistic regression and Minhash

Language: Python - Size: 133 MB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 6 - Forks: 2

AntoineHo/CASH

Compare and shuffle heterozygosity using BED and VCF files

Language: Python - Size: 265 KB - Last synced: 7 months ago - Pushed: almost 3 years ago - Stars: 2 - Forks: 0

raymondkiu/bioinformatics-tools

Small and simple scripts useful for various bioinformatics purposes e.g. extract sequences from fasta files

Language: Shell - Size: 78.1 KB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 14 - Forks: 5

fg6/forACT

Pipeline to prepare alignments for visualization with ACT (goo.gl/1T28jX) and for locating possible inter-chromosomal re-arrengments/misjoints

Language: C++ - Size: 11.6 MB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 2

fg6/seq_factotum

A package for fast genomic sequences manipulation or interrogation

Language: C++ - Size: 141 KB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

tanghaibao/allhic

Genome scaffolding based on HiC data in heterozygous and high ploidy genomes

Language: Jupyter Notebook - Size: 28.6 MB - Last synced: 7 months ago - Pushed: almost 3 years ago - Stars: 56 - Forks: 11

AlBaarS/Nxx_calc

Nxx calculator (N50, N80, N90, etc.) which also gives the respective Lxx and GC content of contigs.

Language: Python - Size: 30.3 KB - Last synced: 9 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 1

merenlab/reads-for-assembly

Simulate metagenomic short reads from one or more populations.

Language: Python - Size: 335 KB - Last synced: about 2 months ago - Pushed: almost 4 years ago - Stars: 23 - Forks: 4

LeonDlugosch/MetaSeq-Toolkit

This pipeline is intended to be a convenient way to work though large sets of metagenomic or metatranscriptiomic datasets while also retaining high analytical flexibility due to retained intermediate results that might be useful outside of the intended purpose.

Language: Shell - Size: 102 MB - Last synced: 4 months ago - Pushed: over 1 year ago - Stars: 4 - Forks: 1

CNuge/snp-placer

Take information about snps on short sequence reads and accurately place the snps in a reference genome

Language: Python - Size: 136 KB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 2 - Forks: 1

lisavader/plasmidEC

An ensemble of plasmid classification tools

Language: Shell - Size: 11.7 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 2 - Forks: 2

zyxue/vr2c

Visualize read-to-contig alignment during assembly analysis

Language: Python - Size: 66.4 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 2 - Forks: 0

bochen0909/hsds-upcxx Fork of Lizhen0909/SpaRC-MPI

hierarchical clustering of DNA sequence using upcxx

Language: C++ - Size: 1.73 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

tmaklin/unmulti

Split a multifasta file into many fasta files containing a single sequence, or extract a list of sequences/contigs. Supports compressed input and output files.

Language: C++ - Size: 33.2 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

haradama/pHash

Software to identify known plasmid sequence from metagenomic assembly using Minhash

Language: Go - Size: 15.9 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 3 - Forks: 0

erg55/Simon-lab-workshop

Learning!

Language: Shell - Size: 307 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 1 - Forks: 4

DaniRuizPerez/SeniorProjectChromevol

BSc Senior Project, Bioinformatics Django web platform for storage and analysis of Biological data. Still in use by the group CHROMEVOL from FIU

Language: Python - Size: 55.4 MB - Last synced: 7 months ago - Pushed: about 4 years ago - Stars: 3 - Forks: 0

algbio/Introduction-to-Applied-Bioinformatics

Genome assembly - From theory to practice (and back)

Size: 2.46 MB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 2 - Forks: 0

schultzm/pandoo

Language: Python - Size: 2.13 MB - Last synced: about 1 month ago - Pushed: over 4 years ago - Stars: 1 - Forks: 2

AntoineHo/COCOA

Coverage Of COntigs Alignment

Language: C++ - Size: 99.1 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

jnarayan81/Palindromer

Explore palindromes

Language: Perl - Size: 328 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

jnarayan81/loopOverSSPACE

Run SSPACE in loop

Language: Perl - Size: 5.86 KB - Last synced: about 1 year ago - Pushed: about 7 years ago - Stars: 0 - Forks: 0