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contigs

Here are 38 public repositories matching this topic...

ablab / quast

Genome assembly evaluation tool

visualization bioinformatics genome-assembly-evaluation contigs

Updated Feb 10, 2022
AMPL

tseemann / abricate

🔎

💊 Mass screening of contigs for antimicrobial and virulence genes

contigs genomic-regions bioinformatics-tool antimicrobial-resistance-genes virulence-genes

Updated Jul 2, 2021
Perl

mcveanlab / mccortex

De novo genome assembly and multisample variant calling

genomics variant-calling kmer cortex genome-analysis genome-assembly de-bruijn-graphs genome-graph contigs

Updated Mar 28, 2019
C

COMBINE-lab / pufferfish

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

genome hash index debruijn dbg contigs debruijn-graph

Updated Mar 8, 2022
C++

lpryszcz / redundans

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

python bioinformatics pipeline genomics assembly docker-image polymorphic gap closing fasta scaffolding assembled-contigs genome-assembly paired-end contigs heterozygous mate-pairs

Updated Nov 15, 2021
Perl

smaegol / PlasFlow

Software for prediction of plasmid sequences in metagenomic assemblies

tensorflow prediction classification fasta plasmid metagenomes contigs metagenome plasmid-sequences metagenome-assembly plasmids plasflow

Updated Jun 28, 2021
Python

platon

oschwengers / platon

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

bioinformatics assembly ngs microbiology bacteria wgs contigs plasmids

Updated Dec 7, 2021
Python

morispi / CONSENT

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

assembly ngs consensus correction long self msa reads contigs long-reads multiple-sequence-alignment polishing self-correction

Updated Oct 13, 2021
C++

tanghaibao / allhic

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

golang pipeline genomics genetic-algorithm hi-c genome-assembly genome-scaffolding contigs polyploid heterozygous lachesis inter-contig-links

Updated May 24, 2021
Jupyter Notebook

Vini2 / GraphBin

GraphBin: Refined binning of metagenomic contigs using assembly graphs

metagenomics binning assembly-graph label-propagation contigs

Updated Nov 21, 2021
Python

merenlab / reads-for-assembly

Simulate metagenomic short reads from one or more populations.

simulation metagenomics fasta fastq contigs

Updated Jun 7, 2020
Python

Vini2 / MetaCoAG

Open

[Feature Request] Custom marker sets as an argument

8

jolespin commented Sep 12, 2021

Hi there! I was hoping that you would eventually make an actual binning tool after I read your GraphBin papers! Looking forward to using this.

One aspect that many binners are lacking is their ability to handle fungus, protists, and sometimes CPR. Though, there's actually decent marker sets for these.

**Would it be possible to include a custom HMM set as an argument for binning tool so we

Read more

enhancement good first issue

Vini2 / GraphBin2

GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs

metagenomics binning contigs assembly-graphs overlapped-binning

Updated Apr 23, 2021
Python

raymondkiu / bioinformatics-tools

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

bioinformatics genome contigs genome-size extract-sequences bioinformatics-tool fasta-files genomeassembly renamecontigs extractcontigs assemblystatistics

Updated Sep 27, 2021
Shell

haradama / PlasmidPicker

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

bioinformatics metagenomics minhash classification logistic-regression fasta contigs metagenome plasmids

Updated Nov 19, 2018
Python

masikol / barapost

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

bioinformatics blast contigs taxonomic-binning nanopore-reads

Updated Nov 19, 2021
Python

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

mysql python trello django bioinformatics database scrum blast contigs unigene clustal

Updated Apr 14, 2020
Python

haradama / pHash

Software to identify known plasmid sequence from metagenomic assembly using Minhash

golang bioinformatics biology metagenomics minhash fasta plasmid contigs metagenome plasmids

Updated Jan 29, 2019
Go

mtisza1 / Cenote_Unlimited_Breadsticks

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

virus discovery prediction hidden-markov-model phage contigs virus-discovery prophage prophage-prediction unlimited-breadsticks

Updated Jun 16, 2021
Shell

CNuge / snp-placer

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

bioinformatics snps genome pandas variant-calling samtools align-dna-sequences contigs

Updated Jun 26, 2020
Python

algbio / Introduction-to-Applied-Bioinformatics

Genome assembly - From theory to practice (and back)

bioinformatics scaffolding genome-assembly unitigs contigs gap-filling error-correction

Updated Apr 1, 2020

schultzm / pandoo

tree pipeline isolate contigs assemblies short-read ruffus

Updated Oct 13, 2019
Python

NCBI-Codeathons / Domain_HMM_Boundaries

Refining Domain Boundaries and Performing Large Scale Parsing

bioinformatics metagenomics bioinformatics-pipeline viruses protein-domains contigs ncbi-virus-discovery-2

Updated Sep 13, 2020
Jupyter Notebook

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

genome transcriptome protein-coding-genes mitochondrial chloroplast contigs plastome genome-skimming

Updated Feb 15, 2021
Perl

zyxue / vr2c

Open

Figure out how to select reads to plot

zyxue commented Aug 19, 2018

https://github.com/zyxue/vr2c/blob/master/vr2c/vr2c.py#L10-L11

Read more

bug good first issue

cpolano / phytoassembly

Sequencing of unculturable plant pathogens

sequencing blast bioperl samtools bwa contigs phytopathology plant-pathogens a5-pipeline

Updated Nov 5, 2018
Shell

AntoineHo / CASH

Compare and shuffle heterozygosity using BED and VCF files

assembly vcf comparison variants bed contigs heterozygosity defined-regions

Updated Jun 7, 2021
Python

erg55 / Simon-lab-workshop

Learning!

cluster assembly loop alignment blast contigs blast-database

Updated Dec 15, 2021
Shell

omercelik-cs / dna-contig-generator

bioinformatics de-bruijn-graphs dna-sequences contigs

Updated Aug 29, 2018
Python

fg6 / forACT

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

Updated May 24, 2020
C++

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