A tool for generating consensus long-read assemblies for bacterial genomes
☆222Feb 23, 2026Updated 3 weeks ago
Alternatives and similar repositories for Autocycler
Users that are interested in Autocycler are comparing it to the libraries listed below
Sorting:
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆148Jan 9, 2026Updated 2 months ago
- Reorients assembled microbial sequences☆136Aug 21, 2025Updated 7 months ago
- a short-read polishing tool for long-read assemblies☆211Sep 19, 2025Updated 6 months ago
- Genome size estimation from long read overlaps☆81Mar 9, 2026Updated last week
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆612Feb 18, 2026Updated last month
- Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates☆86Jan 24, 2026Updated last month
- Ultra-fast preprocessing and quality control for long-read sequencing data☆225Sep 6, 2025Updated 6 months ago
- Assemble bacterial isolate genomes from Nanopore reads☆129Jan 22, 2025Updated last year
- A tool for generating consensus long-read assemblies for bacterial genomes☆341Sep 11, 2025Updated 6 months ago
- Plasmid analysis using rearrangement distances☆50Mar 12, 2026Updated last week
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆240Oct 12, 2025Updated 5 months ago
- An updated pipeline for pangenome investigation☆350Jan 15, 2026Updated 2 months ago
- Graph-based assembly phasing☆91Nov 25, 2025Updated 3 months ago
- Bifrost graph gene caller.☆98Jan 20, 2026Updated 2 months ago
- ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.☆298Feb 3, 2026Updated last month
- LexicMap: efficient sequence alignment against millions of prokaryotic genomes☆216Mar 13, 2026Updated last week
- ☆156Jun 18, 2024Updated last year
- Fast pairwise transmission inference from single genome and/or metagenomic data☆24Aug 1, 2025Updated 7 months ago
- Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!☆179Updated this week
- A new high-resolution long-read metagenome assembler for even noisy reads☆124Mar 14, 2026Updated last week
- Rapid determination of appropriate reference genomes.☆100Jan 22, 2025Updated last year
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆44Aug 20, 2025Updated 7 months ago
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids using protein structural information☆42Updated this week
- Precise host read removal☆119Sep 4, 2025Updated 6 months ago
- Split k-mer analysis – version 2☆104Jan 29, 2026Updated last month
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆65Jun 16, 2025Updated 9 months ago
- MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.☆212Mar 3, 2026Updated 2 weeks ago
- Bioinformatics tool for Locus Visualisation☆162Mar 11, 2026Updated last week
- A hybrid assembly and MAG recovery pipeline (and more!)☆104Jan 27, 2026Updated last month
- Read alignment statistics for metagenomics☆392Updated this week
- Recombination-free trees☆63Sep 1, 2025Updated 6 months ago
- Remove human reads from a sequencing run☆48Mar 9, 2026Updated last week
- fast phage annotation program☆199Feb 1, 2026Updated last month
- geNomad: Identification of mobile genetic elements☆296Updated this week
- Strain-level haplotyping for metagenomes with short or long-reads.☆65Apr 10, 2025Updated 11 months ago
- a long read simulator that can imitate many types of read problems☆273Jul 22, 2024Updated last year
- Quickly generate consensus assemblies for bacterial genomes☆14Sep 12, 2025Updated 6 months ago
- k-mers and the like☆22Mar 2, 2026Updated 2 weeks ago
- Compute a pairwise SNP distance matrix from one or two alignment(s)☆26Sep 12, 2024Updated last year