Alternatives and similar repositories for sra-tools

Users that are interested in sra-tools are comparing it to the libraries listed below

• MultiQC / MultiQC
  Aggregate results from bioinformatics analyses across many samples into a single report.
  ☆1,396Updated last week
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,515Updated 6 months ago
• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆1,011Updated 8 months ago
• trinityrnaseq / trinityrnaseq
  Trinity RNA-Seq de novo transcriptome assembly
  ☆877Updated 10 months ago
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆557Updated 2 weeks ago
• OpenGene / fastp
  An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
  ☆2,240Updated 2 weeks ago
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆755Updated 2 weeks ago
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆763Updated last week
• nf-core / rnaseq
  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
  ☆1,163Updated this week
• kblin / ncbi-genome-download
  Scripts to download genomes from the NCBI FTP servers
  ☆1,051Updated 4 months ago
• COMBINE-lab / salmon
  🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
  ☆851Updated last year
• jorvis / biocode
  Bioinformatics code libraries and scripts
  ☆551Updated 4 months ago
• igvteam / igv
  Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
  ☆706Updated this week
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆798Updated last month
• samtools / samtools
  Tools (written in C using htslib) for manipulating next-generation sequencing data
  ☆1,808Updated last week
• samtools / hts-specs
  Specifications of SAM/BAM and related high-throughput sequencing file formats
  ☆690Updated last month
• DerrickWood / kraken2
  The second version of the Kraken taxonomic sequence classification system
  ☆853Updated 2 weeks ago
• ablab / spades
  SPAdes Genome Assembler
  ☆883Updated this week
• pysam-developers / pysam
  Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight…
  ☆870Updated 2 weeks ago
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆533Updated 3 months ago
• samtools / bcftools
  This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.gith…
  ☆825Updated last month
• tseemann / prokka
  Rapid prokaryotic genome annotation
  ☆942Updated last year
• lh3 / minimap2
  A versatile pairwise aligner for genomic and spliced nucleotide sequences
  ☆2,087Updated 2 months ago
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆746Updated 4 months ago
• davidemms / OrthoFinder
  Phylogenetic orthology inference for comparative genomics
  ☆819Updated 4 months ago
• pachterlab / kallisto
  Near-optimal RNA-Seq quantification
  ☆711Updated 2 weeks ago
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆520Updated 3 months ago
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆856Updated 6 months ago
• tanghaibao / jcvi
  Python library to facilitate genome assembly, annotation, and comparative genomics
  ☆878Updated last week
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆851Updated last year