Top 16 fastq open source projects

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.

✭ 31

java shell data-structures fastq deduplication string-search string-similarity hamming umis unique-molecular-identifiers

pheniqs

Fast and accurate sequence demultiplexing

✭ 14

C++python HTML shell c Makefile CSS autocomplete tagging sequencing barcode sam robust tag bam fastq multiplexing cram demultiplexing classifiers

SPLiT-Seq demultiplexing

An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data

✭ 20

python shell scrna-seq single-cell fastq demultiplexing single-cell-rna-seq single-cell-analysis single-cell-omics scrna-seq-analysis single-cell-sequencing split-seq

fastq utils

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

naf

Nucleotide Archival Format - Compressed file format for DNA/RNA/protein sequences

✭ 35

c perl Makefile compression dna file-format protein rna fasta fastq

readfq

A simple tool to calculate reads number and total base count in FASTQ file

✭ 19

ngs fastq

fuc

Frequently used commands in bioinformatics

✭ 23

python visualization api cli bioinformatics sam vcf fasta gtf bed maf bam fastq cram gff

bioinf-commons

Bioinformatics library in Kotlin

✭ 21

kotlin hmm bioinformatics progress methylation dataset fasta chip-seq sampling bed bam dataframe fastq mixture hypothesis-testing 2bit cancellable dna-sequence

fastq-and-furious

Efficient handling of FASTQ files from Python

✭ 49

python c ngs fastq

Command line utility for manipulating Illumina-generated FastQ files.

✭ 31

rust Dockerfile bioinformatics genomics next-generation-sequencing illumina fastq fastq-files

ngs pipeline

Exome/Capture/RNASeq Pipeline Implementation using snakemake

✭ 40

python perl r shell snakemake pipeline panel ngs tophat gatk rnaseq fastq exome ngs-pipeline annovar snpeff

nullarbor

💾 📃 "Reads to report" for public health and clinical microbiology

✭ 111

perl Raku shell HTML CSS PHP Makefile public-health report variant-calling bacteria fastq phylogenomics denovo-assembly genotyping resistome virulome

Pairfq

Sync paired-end FASTA/Q files and keep singleton reads

✭ 18

perl fasta fastq paired-end

bin

My bioinfo toolbox

✭ 42

python shell perl c bioinformatics ngs sam bam filtering fastq

fastqp

Simple FASTQ quality assessment using Python

✭ 101

python bioinformatics sam fastq nucleotide-plot kmer-distribution

cljam

A DNA Sequence Alignment/Map (SAM) library for Clojure

✭ 85

clojure bioinformatics genomics sam vcf fasta bigwig bed bam fastq bcf wig gff 2bit

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