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MultiQC: Aggregate bioinformatics results across many samples into a single report
3m
50K+
1
Software package for assigning SARS-CoV-2 genome sequences to global lineages
4d
1M+
4
Tools (written in C using htslib) for manipulating next-generation sequencing data
2m
1M+
5
Variant calling & manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF
2m
1M+
25
Computational package that contains functions broadly useful for viral amplicon-based sequencing
1y
1M+
Viral Annotation DefineR: classification and annotation of viral sequences
6d
1M+
2
FastQC: A quality control analysis tool for high throughput sequencing data
3y
1M+
2
Kraken2: Taxonomic sequence classifier. Some images with a kraken2 db and some w/out
2m
1M+
5
BBTools suite of tools from Joint Genome Institute
1m
500K+
Pre-process NGS data to prepare for downstream analysis
7y
500K+
Trimmomatic: A flexible read trimming tool for Illumina NGS data
2m
500K+
2
Freyja: recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset
5d
100K+
Automated prokaryotic genome annotation tool
10m
100K+
4
Scan contig files against traditional PubMLST typing schemes (tool from T. Seemann)
1m
100K+
1
SPAdes - de novo DBG genome assembler
2m
100K+
4
Find acquired AMR genes and some point mutations in protein or assembled nucleotide sequences
2m
100K+
1
Burrow-Wheeler Aligner for short-read alignment
1y
50K+
3
Toolkit for processing sequences in FASTA/Q formats
1y
100K+
6
Fast genome and metagenome distance estimation using MinHash http://mash.readthedocs.org
12d
50K+
3
Genome assembly evaluation tool
2y
100K+
1
Faster SPAdes (or SKESA or Velvet) assembly of Illumina reads
9m
100K+
bedtools - the swiss army knife for genome arithmetic
3y
50K+
1
Lyve-SET: a method of using hqSNPs to create a phylogeny
3y
50K+
Mass screening of contigs for AMR, plasmid replication, or virulence genes
5m
50K+