Nextclade
Nextclade: clade assignment, mutation calling and quality control for viral genomes - Published in JOSS (2021)
Multilocus sequence typing by blast from de novo assemblies against PubMLST
Multilocus sequence typing by blast from de novo assemblies against PubMLST - Published in JOSS (2016)
CheckQC
CheckQC: Quick quality control of Illumina sequencing runs - Published in JOSS (2018)
SaffronTree
SaffronTree: Fast, reference-free pseudo-phylogenomic trees from reads or contigs. - Published in JOSS (2017)
biocommons.seqrepo
non-redundant, compressed, journalled, file-based storage for biological sequences
ANCOMBC
Differential abundance (DA) and correlation analyses for microbial absolute abundance data
GFF3toEMBL
GFF3toEMBL: Preparing annotated assemblies for submission to EMBL - Published in JOSS (2016)
hgvs
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
https://github.com/biocommons/bioutils
provides common tools and lookup tables used primarily by the hgvs and uta packages
https://github.com/broadinstitute/gatk
Official code repository for GATK versions 4 and up
isobar
A Python package for creating and manipulating musical patterns, designed for use in algorithmic composition, generative music and sonification. Can be used to generate MIDI events, MIDI files, OSC messages, or custom actions.
scCATCH
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
https://github.com/cbg-ethz/v-pipe
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
https://github.com/cdcgov/tostadas
🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission
nrex
nRex: Germline and somatic single-nucleotide, short indel and structural variant calling
fluentdna
FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.
https://github.com/biojulia/readdatastores.jl
Datastores for reads, not your papa's FASTQ files.
https://github.com/biocommons/seqrepo-rest-service
OpenAPI-based REST interface to biological sequences and sequence metadata
https://github.com/brentp/mosdepth
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
tnpb
Snakemake workflows for TAM depletion analysis and de novo IS605 annotation
dashboard
MOMSI Standard Landscape Review Curation Workflow & Multi-Omics Dashboard
covid-19-signal
Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
16smart
16s rRNA Sequencing Meta-analysis Reproducibility Tool (using mothur).
https://github.com/akikuno/dajin
One-step genotyping software using a long-read sequencer
stitch
Template-based assembly of proteomics short reads for de novo antibody sequencing and repertoire profiling
pyigmap
[UNDER DEVELOPMENT] Pipeline for mapping and annotating T- and B-cell receptor gene rearrangement sequences
sammyseq
Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.
https://github.com/biocommons/anyvar
[in development] Proof-of-Concept variation translation, validation, and registration service
zarp-cli
A user-friendly command-line interface for the ZARP RNA-seq analysis workflow
assemblebac
avantonder/assembleBAC is a bioinformatics best-practise analysis pipeline for assembling and annotating bacterial genomes.
https://github.com/charlesfoster/ont-analysis-toolkit
A toolkit for monitoring ONT MinION sequencing, followed by data analysis, for viral genomes amplified with tiled amplicon sequencing.
metaboverse
Visualization and analysis platform for metabolic data and network pattern recognition