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C++ |
22 |
Simple convertor from bam to FASTQ |
Apr 17, 2023 |
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|
Python |
26 |
Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files. |
Aug 11, 2022 |
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|
Perl |
47 |
A collection of scripts developed to interact with fasta, fastq and sam/bam files. |
Apr 18, 2022 |
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|
Python |
29 |
Read and write FASTQ and FASTA efficiently from Python |
Aug 11, 2022 |
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|
Rust |
3 |
Extract protein and DNA k-mers from FASTA/FASTQ files |
Jul 20, 2020 |
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|
Shell |
5 |
Optimised pipeline to process whole genome sequence data from fastq to BAM on NCI Gadi |
Mar 22, 2022 |
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C |
2 |
A simple program to split sequences from a FASTA/FASTQ file into k-mers in the FASTA … |
Dec 15, 2021 |
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Julia |
26 |
(No maintenance) Detect gene fusion directly from raw fastq files |
Mar 09, 2023 |
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Perl |
48 |
Tool set for processing fasta/fastq/table formated data. Usually they are perl scripts. |
Apr 13, 2023 |
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Python |
4 |
Genomic Dataset Constructor: create example BED, GFF, SAM, FASTQ files from "ASCII art" definitions |
Sep 22, 2016 |
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Rust |
3 |
A fast bioinformatics tool for (colored) cDBG construction from reads in .fasta and .fastq formats |
Oct 14, 2022 |
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R |
2 |
Filtering missing data from a fasta alignment |
Jul 27, 2021 |
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Nextflow |
3 |
Nextflow pipeline for CNest |
Mar 31, 2022 |
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Nextflow |
4 |
None |
Jan 12, 2022 |
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|
Nextflow |
4 |
MTBSeq made simple and easy using Nextflow. |
Apr 09, 2022 |
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Nextflow |
4 |
Polygenic Risk Scores Pipeline to calculate genetic risk score for any given phenotype/trait (using PRSice) |
Mar 02, 2022 |
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|
Nextflow |
4 |
The Donald Danforth Plant Science Center Bioinformatics Core Facility public repository |
Mar 02, 2020 |
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Nextflow |
4 |
A simple nextflow pipeline for Illumina run metrics (InterOp) and generation of fastq files (bcl2fastq) |
May 03, 2022 |
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Nextflow |
4 |
A simple fastp-MultiQC nextflow pipeline |
Jul 13, 2022 |
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Nextflow |
4 |
An SARS-CoV-2 bioinformatics pipeline for CLIA validation using Dr. Erin Young's Cecret StaphB pipeline as … |
Jan 20, 2022 |
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|
Nextflow |
4 |
A proof of concept RNA-Seq pipeline with Nextflow |
Dec 20, 2018 |
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|
Nextflow |
4 |
Workflow leveraging the scanpy-scripts package to run Scanpy in a Nextflow workflow |
Dec 03, 2020 |
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Nextflow |
4 |
Quantification component for droplet-based studies |
Nov 17, 2021 |
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Nextflow |
4 |
None |
Jul 20, 2022 |
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|
Nextflow |
4 |
Nextflow training material for FAANG workshop February 2020 |
Apr 29, 2021 |
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|
Nextflow |
4 |
Nextflow pipeline for BWA, BWA2 and STAR alignments |
May 07, 2022 |
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|
Nextflow |
4 |
Nextflow pipeline for the preprocessing of BAM files based on GATK best practices. Marking duplicates, … |
Jul 18, 2022 |
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|
Nextflow |
4 |
[WIP] Evaluate outcomes from genome editing experiments |
Jul 14, 2022 |
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|
Nextflow |
4 |
Quantitative shotgun MS proteomics |
May 05, 2022 |
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|
Nextflow |
4 |
A pipeline to investigate horizontal gene transfer from NGS data |
Jun 28, 2022 |
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Nextflow |
4 |
Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric … |
Jun 29, 2022 |
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|
Nextflow |
4 |
SLAMSeq processing and analysis pipeline |
Aug 29, 2021 |
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|
Nextflow |
4 |
None |
May 25, 2022 |
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|
Nextflow |
4 |
FTW |
Aug 23, 2022 |
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|
Nextflow |
4 |
None |
May 22, 2019 |
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|
Nextflow |
5 |
Spriggan is a pipeline used for assembly of bacterial whole genome sequence data and identification … |
Jan 18, 2022 |
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|
Nextflow |
5 |
GENE-SWitCH project RNA-Seq analysis pipeline |
Jun 14, 2022 |
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|
Nextflow |
5 |
ELIXIR VIB-CRG courses on containers (Docker + Singularity) and Nextflow. |
Jan 10, 2022 |
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|
Nextflow |
5 |
Single cell transcriptome analysis pipeline based on DropEst |
Sep 15, 2020 |
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|
Nextflow |
5 |
Coprolite host Identification pipeline |
Aug 18, 2021 |
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|
Nextflow |
5 |
Nextflow pipeline encapsulating workflows for analyzing expansion lattice light-sheet microscopy (ExLLSM) imagery |
May 26, 2022 |
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|
Nextflow |
5 |
None |
Dec 14, 2021 |
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|
Nextflow |
5 |
Assessing the quality of prokaryotic genomes, filtering and dereplication |
Apr 07, 2022 |
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|
Nextflow |
6 |
Pipeline to build a massive tree from global data |
May 24, 2022 |
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|
Nextflow |
6 |
None |
Jun 11, 2022 |
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|
Nextflow |
6 |
Slow-paced containers and Nextflow course for beginners. |
Jun 20, 2022 |
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|
Nextflow |
6 |
Quality control pipeline for RamDA-seq experiments. |
Dec 03, 2020 |
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|
Nextflow |
6 |
Validation studies for docking related studies |
Nov 20, 2021 |
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|
Nextflow |
6 |
Easy & parallel download of FASTQ files from public repositories (SRA, EGA, GDC) |
Nov 22, 2021 |
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|
Nextflow |
7 |
Small variant calling for human samples |
Jul 30, 2022 |