|
|
Groovy |
2 |
Small variant calling for haploid samples |
Apr 25, 2022 |
|
|
Nextflow |
11 |
Assembly and intrahost / low-frequency variant calling for viral samples |
May 20, 2020 |
|
|
Nextflow |
74 |
Assembly and intrahost/low-frequency variant calling for viral samples |
Aug 19, 2022 |
|
|
None |
14 |
FermiKit small variant calls for public SGDP samples |
Aug 03, 2021 |
|
|
None |
2 |
Variant-Calling-Example |
Apr 20, 2023 |
|
|
Python |
46 |
Benchmarking toolkit for variant calling |
Mar 08, 2023 |
|
|
Python |
2 |
Variant calling workflow for mixed ploidy samples implemented in Snakemake and using GATK4 |
Apr 24, 2024 |
|
|
Shell |
4 |
H3A variant calling pipeline |
Apr 20, 2021 |
|
|
Cython |
8 |
TIDDIT - structural variant calling |
Jun 03, 2022 |
|
|
Python |
2 |
variant calling and processing |
Apr 27, 2022 |
|
|
Cython |
52 |
TIDDIT - structural variant calling |
Mar 26, 2023 |
|
|
R |
6 |
Tumor-only variant calling |
May 17, 2023 |
|
|
Python |
29 |
10x Genomics Linked-Read Alignment, Variant Calling, Phasing, and Structural Variant Calling |
Feb 15, 2023 |
|
|
Python |
931 |
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis |
May 19, 2023 |
|
|
Jupyter Notebook |
4 |
A bioinformatic variant calling pipeline |
Aug 24, 2017 |
|
|
Nextflow |
9 |
gatk4 RNA variant calling pipeline |
Aug 02, 2022 |
|
|
HTML |
5 |
Nextflow Tutorial - Variant Calling Edition |
Jul 18, 2022 |
|
|
Shell |
2 |
Variant calling and PSMC workflows |
Oct 22, 2023 |
|
|
Scala |
3 |
Tools for comparing somatic variant calling tools. |
May 20, 2021 |
|
|
None |
5 |
SNP and variant calling pipeline for bacteria |
Feb 02, 2023 |
|
|
Python |
3 |
Snakemake pipeline for variant calling using GATK |
Mar 02, 2023 |
|
|
C |
10 |
TOPMed Freeze 3 variant calling pipeline |
Nov 24, 2021 |
|
|
None |
2 |
Consensus assembly and variant calling workflow |
Aug 17, 2017 |
|
|
None |
15 |
Minor Variant Calling and Phasing Tools |
Jul 31, 2022 |
|
|
Shell |
20 |
Variant Calling Pipeline in Cromwell/WDL |
Nov 13, 2020 |
|
|
C++ |
21 |
Interface to various variant calling formats. |
Apr 19, 2022 |
|
|
None |
12 |
Consensus assembly and variant calling workflow. |
Oct 27, 2022 |
|
|
Python |
5 |
Andersen Lab Python-based pipeline for variant calling. |
Jan 28, 2023 |
|
|
Python |
60 |
Variant calling tool for long-read sequencing data |
May 02, 2023 |
|
|
Nextflow |
3 |
Variant calling pipeline for the Illumina Dragen platform |
Apr 17, 2023 |
|
|
Python |
2 |
Snakemake pipeline for read mapping and variant calling |
Sep 08, 2022 |
|
|
R |
5 |
Automated Pipeline for Variant/Haplotype Calling and Filtering |
May 13, 2023 |
|
|
Python |
2 |
Validate prioritization of tumor-only variant calling |
Jun 04, 2016 |
|
|
Nextflow |
12 |
Nextflow pipeline for Mutect2 somatic variant calling best practices |
Jul 14, 2022 |
|
|
Python |
3 |
Multisample DNAseq variant calling pipeline for use in diagnostics |
Mar 11, 2021 |
|
|
wdl |
6 |
WDL workflows for variant calling and assembly using ONT |
Apr 19, 2023 |
|
|
R |
2 |
Wrapper and analysis scripts for RNA variant calling pipeline |
Nov 19, 2023 |
|
|
Perl |
11 |
A wrapper for calling small variants from human germline high-coverage single-sample Illumina data |
Sep 24, 2021 |
|
|
Python |
4 |
Code Samples for calling the Intrinio API |
May 26, 2019 |
|
|
Nextflow |
3 |
Nextflow pipeline for CNest |
Mar 31, 2022 |
|
|
Nextflow |
4 |
None |
Jan 12, 2022 |
|
|
Nextflow |
4 |
MTBSeq made simple and easy using Nextflow. |
Apr 09, 2022 |
|
|
Nextflow |
4 |
*de novo* orthologous gene predictions from bam + bed or fasta/fastq data |
Jul 22, 2021 |
|
|
Nextflow |
4 |
Polygenic Risk Scores Pipeline to calculate genetic risk score for any given phenotype/trait (using PRSice) |
Mar 02, 2022 |
|
|
Nextflow |
4 |
The Donald Danforth Plant Science Center Bioinformatics Core Facility public repository |
Mar 02, 2020 |
|
|
Nextflow |
4 |
A simple nextflow pipeline for Illumina run metrics (InterOp) and generation of fastq files (bcl2fastq) |
May 03, 2022 |
|
|
Nextflow |
4 |
A simple fastp-MultiQC nextflow pipeline |
Jul 13, 2022 |
|
|
Nextflow |
4 |
An SARS-CoV-2 bioinformatics pipeline for CLIA validation using Dr. Erin Young's Cecret StaphB pipeline as … |
Jan 20, 2022 |
|
|
Nextflow |
4 |
A proof of concept RNA-Seq pipeline with Nextflow |
Dec 20, 2018 |
|
|
Nextflow |
4 |
Workflow leveraging the scanpy-scripts package to run Scanpy in a Nextflow workflow |
Dec 03, 2020 |