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Search results for perl sequencing

61 search results found

Sars Cov 2_sequencing ⭐ 333

A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.

Rapid large-scale prokaryote pan genome analysis

Mirdeep2 ⭐ 120

Discovering known and novel miRNAs from small RNA sequencing data

Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.

Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data

Ascatngs ⭐ 46

Somatic copy number analysis using WGS paired end wholegenome sequencing

Snpsplit ⭐ 43

Allele-specific alignment sorting

Assembly_improvement ⭐ 39

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

Cnvcaller ⭐ 37

Bac Genomics Scripts ⭐ 28

Collection of scripts for bacterial genomics

RNASeq pipeline

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.

an empirical Bayesian framework for mutation detection from cancer genome sequencing data

Variant Filter ⭐ 25

A false-positive filter for variants called from massively parallel sequencing

Dna Me Pipeline ⭐ 24

DCC/DAC methylation pipeline source

Bioinf2019 ⭐ 23

MONOD2 is a toolkit for methylation haplotype analysis of bisulfite sequencing data

Versatile simulator for structural variance and Nanopore/PacBio sequencing reads

Expanded STR algorithm for Illumina sequencing data

A Better Sequencing Simulator for Metagenomics

A Modern Perl Framework for High Throughput Sequencing analysis

Plasmidseeker ⭐ 18

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

Bio Tradis ⭐ 15

A set of tools to analyse the output from TraDIS analyses

Mlst_check ⭐ 14

Multilocus sequence typing by blast using the schemes from PubMLST

Distribution Based Clustering ⭐ 14

Extremely accurate algorithm used to group DNA sequences from microbial communities into operational taxonomic units (proxy for species) for ecological or biomedical research. This algorithm uses the information contained in the distribution of DNA sequences across samples along with sequence similarity to cluster sequences more accurately than other methods that are currently available. Developed for Illumina next-generation sequencing libraries, but applicable to any sequencing platform with s

A straightforward and complete next-generation sequencing read simulator

Parsecnv2 ⭐ 14

Parse Copy Number Variation from Array and Sequencing

Hlaprofiler ⭐ 14

Using k-mers to call HLA alleles in RNA sequencing data

Sars Cov 2_multi Pcr_v1.0 ⭐ 12

SARS-CoV-2 analysis pipeline for multiplex-PCR MPS(Massive Parrallel Sequencing) data

Scisa Tools ⭐ 12

single-cell-Isoform-Sequencing-Analysis-Tools: New and powerful tools brings single-cell RNA sequencing to the Isoform level and single molecule resolution.

Ervcaller ⭐ 11

ERVcaller is a tool designed to accurately detect and genotype non-reference unfixed endogenous retroviruses (ERVs) and other transposable elements (TEs) in the human genome using next-generation sequencing (NGS) data. We evaluated the tools using both simulated and real benchmark whole-genome sequencing (WGS) datasets. ERVcaller is capable to accurately detect various TE insertions of any lengths, particularly ERVs. It allows for the use of a TE reference library regardless of sequence complexi

Imonitor ⭐ 11

This script use to analyze the immune repertoire sequenced by high throughtput sequencing

Scbs Map ⭐ 11

Single-cell Bisulfite Sequencing Data Mapping

hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data

TEMP is a software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data

Autoadapt ⭐ 11

Automatic quality control for FASTQ sequencing files

Illumina analysis pipeline

Diversitools ⭐ 10

Tool for analysing viral diversity from High Throughput Sequencing

Damidseq_pipeline ⭐ 10

An automated pipeline for processing DamID sequencing datasets

NGS perl modules

Indelseek ⭐ 10

Detect complex indels from next-generation sequencing reads

Bugbuilder ⭐ 10

Hands-free microbial genome assembly

Biogrinder ⭐ 9

Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.

Npg_seq_pipeline ⭐ 9

Processing and analysis of data coming from Illumina sequencing machines

FLT3 ITD detection (ITDseek) and simulation (ITDsim)

Megamerge ⭐ 8

MeGAMerge (A tool to merge assembled contigs, long reads from metagenomic sequencing runs)

Targeted Amplicon Bisulfite Sequencing Analysis Tool

Combine structural variation outputs from long sequencing reads into a superior call set

Metagenome Assembly And Binning ⭐ 7

Current workflows in the symbiosis department

Cg Pipeline ⭐ 6

Genome assembly/prediction/annotation pipeline for the Linux command line

Perlprimer ⭐ 6

Primer design for standard PCR, bisulphite PCR, QPCR and sequencing

Rna Seq Scripts ⭐ 6

This is a collection of small scripts built by the Lenz lab to make RNA sequencing tasks more efficient.

software for analysis of chromatin feature occupancy profiles from high-throughput sequencing data

Metaprism ⭐ 5

Taxonomical and Functional Profiling for Shotgun Metagenomic Sequencing

Bioinformatic software for TAPS DNA methylation sequencing

Tools for analysis of RAD Sequencing data

QC checks and metrics for Illumina NGS data

Decontaminer ⭐ 5

DecontaMiner is a tool designed and developed to investigate the presence of contaminating sequences in unmapped NGS data. It can suggest the presence of contaminating organisms in sequenced samples, that might derive either from laboratory contamination or from their biological source, and in both cases can be considered as worthy of further investigation and experimental validation. The novelty of DecontaMiner is mainly represented by its easy integration with the standard procedures of NGS da

Umi Grinder ⭐ 5

The use of UMIs for sequencing becomes more and more frequently used so we need to take them into consideration when deduplicating data aligning to the same positions

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