contigs

There are 1 repository under contigs topic.

ablab / quast
Genome assembly evaluation tool
bioinformatics genome-assembly-evaluation visualization contigs
Language:AMPL 366
tseemann / abricate
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
antimicrobial-resistance-genes virulence-genes contigs bioinformatics-tool genomic-regions
Language:Perl 338
Gabaldonlab / redundans
Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
genome-assembly python pipeline fasta contigs heterozygous polymorphic docker-image mate-pairs paired-end assembled-contigs gap closing scaffolding bioinformatics assembly genomics
Language:C++ 124
mcveanlab / mccortex
De novo genome assembly and multisample variant calling
genome-assembly de-bruijn-graphs kmer cortex variant-calling genome-graph contigs genome-analysis genomics
Language:C 110
COMBINE-lab / pufferfish
An efficient index for the colored, compacted, de Bruijn graph
contigs dbg debruijn debruijn-graph genome hash index
Language:C 107
platon
oschwengers / platon
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
microbiology bioinformatics plasmids ngs wgs contigs bacteria assembly
Language:Python 99
tobiasrausch / wally
Wally: Visualization of aligned sequencing reads and contigs
genomics sequencing visualization alignment sequencing-data mapping plotting assembly contigs
Language:C++ 97
smaegol / PlasFlow
Software for prediction of plasmid sequences in metagenomic assemblies
classification contigs fasta metagenome metagenome-assembly metagenomes plasflow plasmid plasmid-sequences plasmids prediction tensorflow
Language:Python 92
metagentools / GraphBin
✨🧬 Refined binning of metagenomic contigs using assembly graphs
metagenomics binning contigs assembly-graph label-propagation
Language:Python 81
tanghaibao / allhic
Genome scaffolding based on HiC data in heterozygous and high ploidy genomes
contigs genetic-algorithm genome-assembly genome-scaffolding genomics golang heterozygous hi-c inter-contig-links lachesis pipeline polyploid
Language:Jupyter Notebook 57
nf-core / funcscan
(Meta-)genome screening for functional and natural product gene sequences
nextflow workflow pipeline assembly contigs function screening metagenomics natural-products antimicrobial-resistance-genes antimicrobial-peptides biosynthetic-gene-clusters bioinformatics amp antibiotic-resistance arg bgc secondary-metabolites amr nf-core
Language:Nextflow 56
morispi / CONSENT
Scalable long read self-correction and assembly polishing with multiple sequence alignment
ngs correction long-reads long reads self-correction self msa multiple-sequence-alignment consensus contigs assembly polishing
Language:C++ 54
metagentools / MetaCoAG
🚦🧬 Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs
binning metagenomics contigs assembly-graphs
Language:Python 42
metagentools / GraphBin2
☯️🧬 Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs
metagenomics binning contigs assembly-graphs overlapped-binning
Language:Python 27
merenlab / reads-for-assembly
Simulate metagenomic short reads from one or more populations.
contigs fasta fastq metagenomics simulation
Language:Python 24
raymondkiu / bioinformatics-tools
Small and simple scripts useful for various bioinformatics purposes e.g. extract sequences from fasta files
extract-sequences fasta-files contigs genome genome-size bioinformatics renamecontigs extractcontigs assemblystatistics genomeassembly bioinformatics-tool
Language:Shell 19
haradama / PlasmidPicker
Software to identify plasmid sequence data from metagenome using logistic regression and Minhash
plasmids fasta bioinformatics metagenomics metagenome contigs minhash logistic-regression classification
Language:Python 6
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.
metagenomics assembly contigs dna binning gene-classification ecology microbiome-analysis micobiome sequencing mapping
Language:Shell 6
mtisza1 / Cenote_Unlimited_Breadsticks
DEPRECATED: Discover divergent virus sequences, prune flanking cellular sequences, make basic report
unlimited-breadsticks virus contigs discovery prediction prophage phage hidden-markov-model virus-discovery prophage-prediction
Language:Shell 6
masikol / barapost
Toolkit for binning FASTA, FASTQ and FAST5 files according to taxonomic annotation
taxonomic-binning nanopore-reads contigs bioinformatics blast
Language:Python 4
algbio / Introduction-to-Applied-Bioinformatics
Genome assembly - From theory to practice (and back)
bioinformatics genome-assembly contigs unitigs scaffolding gap-filling error-correction
3
CNuge / snp-placer
Take information about snps on short sequence reads and accurately place the snps in a reference genome
bioinformatics samtools snps align-dna-sequences genome contigs pandas variant-calling
Language:Python 3
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
django contigs blast trello scrum database mysql bioinformatics clustal unigene python
Language:Python 3
haradama / pHash
Software to identify known plasmid sequence from metagenomic assembly using Minhash
bioinformatics fasta metagenomics metagenome minhash biology plasmids plasmid contigs golang
Language:Go 3
lisavader / plasmidEC
An ensemble of plasmid classification tools
bioinformatics plasmids bacteria ngs contigs ensemble-classifier ecoli
Language:Shell 3
quxiaojian / get_cp_and_mt_genes_from_contigs_of_genome-skimming_or_transcriptome_data
get chloroplast and mitochondrial genes from contigs of genome-skimming or transcriptome data
plastome transcriptome protein-coding-genes genome-skimming mitochondrial chloroplast genome contigs
Language:Perl 3
AntoineHo / CASH
Compare and shuffle heterozygosity using BED and VCF files
heterozygosity vcf bed contigs comparison assembly defined-regions variants
Language:Python 2
zyxue / vr2c
Visualize read-to-contig alignment during assembly analysis
genome-assembly transcriptome-assembly contig-coverage contigs alignment read-to-contig-alignment
Language:Python 2
cpolano / phytoassembly
Sequencing of unculturable plant pathogens
sequencing a5-pipeline bioperl bwa samtools blast contigs plant-pathogens phytopathology
Language:Shell 1
erg55 / Simon-lab-workshop
Learning!
blast blast-database assembly loop cluster contigs alignment
Language:Shell 1
NCBI-Codeathons / Domain_HMM_Boundaries
Refining Domain Boundaries and Performing Large Scale Parsing
ncbi-virus-discovery-2 metagenomics protein-domains viruses contigs bioinformatics bioinformatics-pipeline
Language:Jupyter Notebook 1
schultzm / pandoo
assemblies contigs isolate pipeline ruffus short-read tree
Language:Python 1
bochen0909 / hsds-upcxx
hierarchical clustering of DNA sequence using upcxx
hierarchical-clustering dna-sequences reads contigs binning
Language:C++ 0
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.
bioinformatics bioinformatics-pipeline bioinformatics-tool blast blastp contigs denovo-assembly genomics genomics-data next ngs ngs-analysis ngs-pipeline sequencer trimmomatic velvet-assembler wgs whole-genome-sequencing
Language:HTML 0
AntoineHo / COCOA
Coverage Of COntigs Alignment
coverage contigs assembly genome bioinformatics visualisation bam sam
Language:C++
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.
fasta c-plus-plus bioinformatics-tool contigs multifasta
Language:C++