eager
masurca
eager | masurca | |
---|---|---|
1 | 1 | |
124 | 229 | |
1.6% | - | |
7.6 | 3.5 | |
10 days ago | 2 months ago | |
Nextflow | M4 | |
MIT License | GNU General Public License v3.0 only |
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eager
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Generate consensus FASTA files pipeline
So after a lot of reading and talking with some people i was able to do it with the eager pipeline (https://github.com/nf-core/eager) migth be a bit dificult to set up, but it is really useful. I leave this here for you and other people that may see this ;)
masurca
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Nanopore long read assembly help!
Hybrid assembly: https://github.com/alekseyzimin/masurca
What are some alternatives?
SqueezeMeta - A complete pipeline for metagenomic analysis
deepvariant - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
mag - Assembly and binning of metagenomes
bioinformatics - Bioinformatic algorithms for the UCLA Bioinformatics Specialization
sarek - Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
patterns - A curated collection of Nextflow implementation patterns
Trycycler - A tool for generating consensus long-read assemblies for bacterial genomes
configs - Config files used to define parameters specific to compute environments at different Institutions
aviary - A hybrid assembly and MAG recovery pipeline (and more!)
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
pyrodigal - Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!