32 results found Sort:

OpenGene
fastp OpenGene
334
1.8k
mit
50
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
qc ngs umi fastq polyg filter adapter merging overlap quality illumina trimming filtering splitting sequencing duplication preprocessing bioinformatics quality-control
Created 2017-10-31
448 commits to master branch, last one 2 months ago
shenwei356
seqkit shenwei356
157
1.2k
mit
26
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
tool fasta fastq golang toolkit sequence manipulation bioinformatics cross-platform
Created 2016-02-28
809 commits to master branch, last one about a month ago
torognes
vsearch torognes
122
642
other
44
Versatile open-source tool for microbiome analysis
fasta fastq search chimera amplicon clustering microbiome metagenomics metabarcoding bioinformatics sequence-alignment
Created 2014-05-16
1,919 commits to master branch, last one about a month ago
seqan
seqan3 seqan
81
391
other
24
The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
blast cpp17 cpp20 fasta fastq seqan modern fm-index samtools cpp-concepts bioinformatics sequence-analysis sequence-alignment
Created 2016-04-04
6,669 commits to main branch, last one 18 days ago
sdparekh
zUMIs sdparekh
67
267
gpl-3.0
13
zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
dge umi fastq rnaseq rna-seq barcodes pipeline expression single-cell
Created 2017-06-20
291 commits to main branch, last one about a year ago
lmdu
pyfastx lmdu
20
246
mit
7
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
dna fasta fastq genome python biology assembly sequence bioinformatics
Created 2019-03-19
604 commits to master branch, last one 3 months ago
mbhall88
rasusa mbhall88
17
195
mit
7
Randomly subsample sequencing reads
bam rust fasta fastq random coverage alignment downsample subsampling bioinformatics genome-analysis
Created 2019-09-26
225 commits to main branch, last one about a month ago
igordot
genomics igordot
54
192
unknown
6
A collection of scripts and notes related to genomics and bioinformatics
dna gtf vcf fast5 fasta fastq science genomics illumina nanopore workflow sequencing bioinformatics
Created 2015-12-22
115 commits to master branch, last one about a year ago
Genetalks
gtz Genetalks
39
169
other
17
A high performance and compression ratio compressor for genomic data, powered by GTXLab of Genetalks.
bam gtx sam gene fastq pacbio compress nanopore compression compression-rate fastq-compression genomic-data-compression
Created 2016-11-11
824 commits to master branch, last one 2 years ago
divonlan
genozip divonlan
11
151
other
1
A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too
bam bwa gvf sam vcf cram gzip bgzip fasta fastq 23andme genomics samtools compression
Created 2019-12-15
3,250 commits to master branch, last one 4 days ago
vanheeringen-lab
seq2science vanheeringen-lab
26
148
mit
6
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
ngs sra fastq rna-seq atac-seq chip-seq pipeline snakemake workflows bioinformatics reproducible-research bioinformatics-pipeline
Created 2019-07-11
1,483 commits to master branch, last one 4 months ago
OpenGene
MutScan OpenGene
38
147
mit
22
Detect and visualize target mutations by scanning FastQ files directly
ngs fastq cancer somatic variant mutation detection validation visualization bioinformatics
Created 2016-07-23
259 commits to master branch, last one 2 years ago
ngless-toolkit
ngless ngless-toolkit
25
142
other
11
NGLess: NGS with less work
bwa ngs fastq haskell science genomics samtools fastq-format metagenomics bioinformatics haskell-language bioinformatics-pipeline next-generation-sequencing
Created 2013-01-08
2,450 commits to main branch, last one about a month ago
tseemann
nullarbor tseemann
37
131
gpl-2.0
20
:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
fastq report bacteria virulome resistome genotyping phylogenomics public-health denovo-assembly variant-calling
Created 2015-01-08
354 commits to master branch, last one 3 years ago
nf-core
fetchngs nf-core
69
127
mit
95
Pipeline to fetch metadata and raw FastQ files from public databases
ena geo sra ddbj fastq nf-core synapse download nextflow pipeline workflow
Created 2021-06-03
1,079 commits to master branch, last one 3 months ago
mdshw5
fastqp mdshw5
14
107
mit
6
Simple FASTQ quality assessment using Python
sam fastq python bioinformatics nucleotide-plot kmer-distribution
Created 2013-09-23
180 commits to master branch, last one 3 years ago
telatin
seqfu2 telatin
7
102
gpl-3.0
3
:rocket: seqfu - Sequece Fastx Utilities
ngs fasta fastq bioconda genomics sequencing bioinformatics bioinformatics-tool
Created 2020-11-26
584 commits to main branch, last one 21 days ago
chrovis
cljam chrovis
12
90
apache-2.0
11
A DNA Sequence Alignment/Map (SAM) library for Clojure
bam bcf bed gff sam vcf wig 2bit cram fasta fastq bigwig clojure genomics bioinformatics
Created 2014-01-08
1,593 commits to master branch, last one 2 days ago
fulcrumgenomics
fqgrep fulcrumgenomics
4
90
mit
13
Grep for FASTQ files
rust fastq genomics bioinformatics
Created 2021-10-12
22 commits to main branch, last one about a year ago
stjude-rust-labs
fq stjude-rust-labs
5
68
mit
15
Command line utility for manipulating Illumina-generated FASTQ files.
rust fastq genomics illumina fastq-files bioinformatics next-generation-sequencing
Created 2018-03-12
413 commits to master branch, last one 6 months ago
markschl
seq_io markschl
11
68
mit
5
FASTA and FASTQ parsing in Rust
rust fasta fastq fastx parser
Created 2017-07-31
123 commits to main branch, last one 10 months ago
BioJulia
FASTX.jl BioJulia
18
60
mit
9
Parse and process FASTA and FASTQ formatted files of biological sequences.
bio fasta fastq julia parsing biojulia fasta-files fastq-files file-format fasta-format fastq-format
Created 2018-10-05
123 commits to master branch, last one 2 days ago
Daniel-Liu-c0deb0t
UMICollapse Daniel-Liu-c0deb0t
7
57
mit
3
Accelerating the deduplication and collapsing process for reads with Unique Molecular Identifiers (UMI). Heavily optimized for scalability and orders of magnitude faster than a previous tool.
java umis fastq hamming deduplication string-search data-structures string-similarity unique-molecular-identifiers
Created 2019-02-25
99 commits to master branch, last one 2 months ago
muellan
metacache muellan
12
56
gpl-3.0
7
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
fasta fastq genome refseq taxonomy long-reads metagenomes ncbi-refseq metagenomics read-mapping dna-sequences bioinformatics classification metagenomic-data short-read-mapper bioinformatics-tool metagenomic-analysis genomic-data-analysis bioinformatics-algorithms metagenomic-classification
Created 2017-02-07
1,028 commits to master branch, last one 3 months ago
StevenWingett
FastQ-Screen StevenWingett
15
55
gpl-3.0
4
Detecting contamination in NGS data and multi-species analysis
bwa ngs fastq bowtie bowtie2 detection metagenomics contamination
Created 2018-08-06
83 commits to master branch, last one about a year ago
KirillKryukov
naf KirillKryukov
6
54
zlib
4
Nucleotide Archival Format - Compressed file format for DNA/RNA/protein sequences
dna rna fasta fastq protein compression file-format
Created 2018-12-11
226 commits to master branch, last one 2 years ago
lgautier
fastq-and-furious lgautier
5
50
mit
2
Efficient handling of FASTQ files from Python
ngs fastq python
Created 2017-01-29
164 commits to master branch, last one about a year ago
sbslee
fuc sbslee
5
45
mit
1
Frequently used commands in bioinformatics
api bam bed cli gff gtf maf sam vcf cram fasta fastq visualization bioinformatics
Created 2021-03-26
952 commits to main branch, last one 11 days ago
fastqc-rs
fastqc-rs fastqc-rs
6
35
mit
1
A quality control tool for FASTQ files written in rust
fastq fastqc k-mer-counting sequence-quality sequence-statistics
Created 2021-02-11
67 commits to main branch, last one 7 months ago
ncherric
Iliad ncherric
2
28
mit
1
ILIAD: A suite of automated Snakemake workflows for processing genomic data for downstream applications
vcf cram idat fastq genetics genomics workflow automatic snakemake genomics-data bioinformatics modularization
Created 2023-02-20
153 commits to main branch, last one 6 months ago