Alternatives and similar repositories for msamtools:

Users that are interested in msamtools are comparing it to the libraries listed below

• Kalan-Lab / zol
  zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
  ☆52Updated last month
• EBI-Metagenomics / mettannotator
  ☆62Updated last month
• irycisBioinfo / PATO
  PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
  ☆58Updated last year
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated last year
• snayfach / MAGpurify
  Improvement of metagenome-assembled genomes
  ☆51Updated 4 years ago
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆51Updated 9 months ago
• allind / EukDetect
  ☆48Updated 9 months ago
• SegataLab / panphlan
  PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
  ☆45Updated last year
• gatech-genemark / MetaGeneMark-2
  MetaGeneMark-2: Improved Gene Prediction in Metagenomes
  ☆18Updated 10 months ago
• hildebra / lotus2
  Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
  ☆54Updated 3 weeks ago
• a-h-b / binny
  ☆28Updated last year
• guyleonard / taxdump_edit
  Add new taxa or taxonomic groups to the NCBI Taxdump files
  ☆19Updated 4 years ago
• mtisza1 / Cenote-Taker3
  Discover and annotate the virome
  ☆35Updated 3 months ago
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆40Updated 4 years ago
• arumugamlab / MIntO
  Pipeline for Reproducible and Scalable Integration of Metagenomic and Metatranscriptomic Data
  ☆14Updated this week
• thomazbastiaanssen / Tjazi
  A microbiome analysis toolkit for R
  ☆21Updated last year
• nvelden / geneviewer
  An R package designed for drawing gene arrow maps
  ☆41Updated last week
• lmlui / Jorg
  MAG Circularization Method
  ☆33Updated 2 years ago
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆48Updated 2 years ago
• weisberglab / beav
  BEAV: Bacterial Element Annotation reVamped
  ☆60Updated 2 months ago
• jhawkey / IS_mapper
  IS mapping software
  ☆53Updated 3 years ago
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆48Updated 2 years ago
• xinehc / melon
  Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes
  ☆34Updated last week
• kussell-lab / mcorr
  Inferring bacterial recombination rates from large-scale sequencing datasets.
  ☆42Updated last year
• adamhockenberry / bacphlip
  A python library for predicting phage lifestyle based on genome sequence
  ☆35Updated last year
• SWittouck / SCARAP
  A toolkit for prokaryotic comparative genomics
  ☆40Updated last week
• endixk / ezaai
  EzAAI - High Throughput Prokaryotic AAI Calculator
  ☆37Updated 3 months ago
• xiaoli-dong / metaerg
  ☆41Updated 3 years ago
• biobakery / maaslin3
  MaAsLin3: Microbiome Multivariate Association with Linear Models
  ☆24Updated 2 weeks ago
• EBI-Metagenomics / EukCC
  Tool to estimate genome quality of microbial eukaryotes
  ☆35Updated last week