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Search results for genome fasta

149 search results found

⚡ ♒ Rapid prokaryotic genome annotation

✂️ ⚡ Rapid haploid variant calling and core genome alignment

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.

Gtotree ⭐ 174

A user-friendly workflow for phylogenomics

Aligngraph ⭐ 165

Algorithm for secondary de novo genome assembly guided by closely related references

Randomly subsample sequencing reads to a specified coverage

Novoplasty ⭐ 140

NOVOPlasty - The organelle assembler and heteroplasmy caller

Badread ⭐ 124

a long read simulator that can imitate many types of read problems

Boosting RNA-Seq assemblies with partial or related genomic sequences

Mirdeep2 ⭐ 120

Discovering known and novel miRNAs from small RNA sequencing data

Sibeliaz ⭐ 113

A fast whole-genome aligner based on de Bruijn graphs

SKESA assembler

Get_homologues ⭐ 98

GET_HOMOLOGUES: a versatile software package for pan-genome analysis

Mcclintock ⭐ 83

Meta-pipeline to identify transposable element insertions using next generation sequencing data

Mummer2circos ⭐ 79

Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments

Python package and CLI for whole-genome duplication related analyses

GenMap - Fast and Exact Computation of Genome Mappability

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.

An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.

Jupiterplot ⭐ 54

A Circos-based tool to visualize genome assembly consistency

Metacache ⭐ 49

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome

Prothint ⭐ 45

Protein hint generation pipeline for gene finding in eukaryotic genomes

Fluentdna ⭐ 43

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.

A program to call variants from genome alignment

Gene prediction software

Antonie is an integrated, robust, reliable and fast processor of DNA reads

An ultrafast tool for genome-wide survey of microsatellites and primer design

Uniquekmer ⭐ 33

Generate unique KMERs for every contig in a FASTA file

Mapcaller ⭐ 32

MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes

Bioinf Commons ⭐ 30

Bioinformatics library in Kotlin

PERF is an Exhaustive Repeat Finder

HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes

Spacepharer ⭐ 28

SpacePHARER CRISPR Spacer Phage-Host pAiRs findER

Chromatiblock ⭐ 28

Colinear block visualisation tool

VAPiD: Viral Annotation and Identification Pipeline

Vcf2fasta ⭐ 25

Converts a VCF file to a FASTA alignment provided a reference genome and a GFF file

An approximate sequence pattern matcher for FASTQ/FASTA files.

A draft genome scaffolder that uses multiple reference genomes in a graph-based approach.

Analysing Metagenomic Species (MGS)

Spraynpray ⭐ 25

Rapid and simple taxonomic profiling of genome and metagenome contigs

Metasanity ⭐ 24

Pipeline for major biological analyses.

Public_scripts ⭐ 24

collection of bioinformatic scripts

Order and orientation of complete bacterial genomes

GC Skew Test for Bacterial Genomes

SMBL - SnakeMake Bioinformatics Library. Automatic installation of bioinformatics software in your SnakeMake pipelines.

Swiftortho ⭐ 21

A high performance tool to identify orthologs and paralogs across genomes.

Biohansel ⭐ 21

Rapidly subtype microbial genomes using single-nucleotide variant (SNV) subtyping schemes

Assembler Components ⭐ 20

Components of genome sequence assembly tools

Contiguator ⭐ 20

Bacterial genomes finishing tool for structural insights on draft genomes

whole genome MLST analysis

Read alignment with a multi-genome reference

Assembly based core genome SNP alignments for bacteria

Workshop Popgenome ⭐ 19

Tutorial about R package PopGenome

Plasmidseeker ⭐ 18

A k-mer based program for the identification of known plasmids from whole-genome sequencing reads

Genetic Map Comparison

For original Nature Biotechnology Publication (Q1 2012)

Wgs2ncbi ⭐ 18

Toolkit for preparing genomes for submission to NCBI

BANDITS: Bayesian ANalysis of DIfferenTial Splicing

Report reverse and ambiguous strand SNPs in GWAS data

Nanovar Archived ⭐ 17

Archived version 1.0.2

Genome Annotation Library - A perl toolkit for working with SO compliant genome annotations

Core Genome Alignment ⭐ 16

Scripts to analyze gene content and make a concatenated alignment of core genes from bacterial genomes.

Metagenomics microbial abundance quantification

Salmontools ⭐ 16

Useful tools for working with Salmon output

Transcript to Genome Consistency Network

Storf Reporter ⭐ 15

Package to extract Unannotated Regions from prokaryotic genomes report coding and pseudogenised genes delimited by stop codons - Named StORFs (Stop - Open Reading Frames)

Sars_cov_2 ⭐ 15

Bioinformatics analysis of SARS-CoV-2

Pantools ⭐ 15

Multiphate ⭐ 14

Throughput PhATE processing of draft or finished phage genomes

SVsim: a tool that generates synthetic Structural Variant calls as benchmarks to test/evaluate SV calling pipelines.

Bioinformatics Tools ⭐ 14

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

In silico taxonomic classification of Bacillus cereus group genomes using whole-genome sequencing data

Docker_bwa_aligner ⭐ 13

Docker containers that demonstrate a proof of concept bwa alignment workflow

LAVA: Lightweight Assignment of Variant Alleles

Deepmased ⭐ 13

Deep learning for Metagenome Assembly Error Detection

Varifier ⭐ 13

Variant call verification

Hadoopcnv ⭐ 12

HadoopCNV is a MapReduce-based copy number variation caller for genome sequencing data

Dna Sequence Machine Learning ⭐ 12

Understand DNA structure and how machine learning can be used to work with DNA sequence data.

Crispr Images ⭐ 12

Code for Shipman et al. 2017

Wessim: Whole Exome Sequencing SIMulator using in silico exome capture

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

Reciprocal_smallest_distance ⭐ 11

Reciprocal Smallest Distance (RSD) is a pairwise orthology algorithm that uses global sequence alignment and maximum likelihood evolutionary distance between sequences to accurately detects orthologs between genomes.

Sequencing_for_genetics ⭐ 11

유전학자를 위한 시퀀싱 자료 분석

Playing around with the human genome and Clojure

Microbiome Classifier Pipeline for Pacific Biosciences 16s Data

Illumina Array Protocols ⭐ 11

processing illumina SNP arrays

SEquence ALignment evaluation suite

Irys Scaffolding ⭐ 10

scripts to parse IrysView output

Microbialgenomicsscripts ⭐ 10

A selection of short scripts for analyzing microbial genomes

local ancestry inference tool for low-coverage resequencing data

Dascrubber Wrapper ⭐ 9

Wrapper script for easier read scrubbing with DASCRUBBER

GSAlign: an ultra-fast sequence alignment algorithm for intra-species genome comparison

Snp Mutator ⭐ 9

Generate mutated sequence files from a reference genome.

Simulate next-generation sequencing reads for tumor samples

Pathogendb Pipeline ⭐ 9

Pipeline for genome assembly + annotation for pathogen surveillance

Pseudo Finder ⭐ 9

Detection of pseudogene candidates in bacterial and archaeal genomes.

R package for microbial pangenomics

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