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Search results for assembly fasta

47 search results found

Pyfastx ⭐ 211

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

Soapdenovo2 ⭐ 197

Next generation sequencing reads de novo assembler.

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/g Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:

Novoplasty ⭐ 140

NOVOPlasty - The organelle assembler and heteroplasmy caller

Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads

Vcf Validator ⭐ 125

Validation suite for Variant Call Format (VCF) files, implemented using C++11

Redundans ⭐ 121

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

SKESA assembler

Assembly Stats ⭐ 92

Get assembly statistics from FASTA and FASTQ files

Phased assembly variant caller

A hybrid assembly and MAG recovery pipeline (and more!)

Plasflow ⭐ 61

Software for prediction of plasmid sequences in metagenomic assemblies

The genome assembler that reduces the computational time of human genome assembly from 400,000 CPU hours to 2,000 CPU hours, utilizing long erroneous 3GS sequencing reads and short accurate NGS sequencing reads.

Jupiterplot ⭐ 54

A Circos-based tool to visualize genome assembly consistency

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

Assembly_improvement ⭐ 39

Improve the quality of a denovo assembly by scaffolding and gap filling

Chromosomer ⭐ 30

A reference-assisted assembly tool for producing draft chromosome sequences.

Order and orientation of complete bacterial genomes

Transfuse ⭐ 22

Merge transcriptome assemblies

Assembler Components ⭐ 20

Components of genome sequence assembly tools

Assembly based core genome SNP alignments for bacteria

Kollector ⭐ 19

de novo targeted gene assembly

Bioinformatics Tools ⭐ 14

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

🍊 💫 Trim, circularise and orient long read bacterial genome assemblies

Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of any size. Described in the Bioinformatics journal paper (2020) by Firtina et al. at https://people.inf.ethz.ch/omutlu/pub/apollo-techn

MIX: Combining multiple assemblies from NGS data

Irys Scaffolding ⭐ 10

scripts to parse IrysView output

Pathogendb Pipeline ⭐ 9

Pipeline for genome assembly + annotation for pathogen surveillance

Metag_analysis_workflow ⭐ 8

Hybrid Assembler for Plasmids

maze: match visualizer

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

ARBitR: Assembly Refinement with Barcode-identity-tagged Reads

Genomics_scripts ⭐ 7

an assembly tool for 16S ribosomal RNA recovery from metagenomic data

Script_collection ⭐ 7

Collection of scripts to solve small bioinformatic challenges.

Targeted Assembly of Short Reads

CAARS: Comparative Assembly and Annotation of RNA-Seq data

Mho_analysis ⭐ 6

MHO_001 hybrid read assembly and analysis

Assemblyevaluator ⭐ 5

A simple tool for evaluating a metagenomic assembly

Large-scale 16S gene assembly using metagenomic shotgun sequences

Assemblanalysis ⭐ 5

Analysis scripts to generate Tables and Figures for Assemblathon 1

Characterize_neisseria_capsule ⭐ 5

Python script to characterize the Neisseria capsule and predict serogroup for Neisseria meningitidis

Assessing genome assemblies using K-mer copies in assemblies and K-mer abundance in Illumina reads

Assemblosis ⭐ 5

CWL-based automated bioinformatics workflow for PacBio and Illumina data

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