An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for chimeric reads, and non-biotinylated fragment pull down in mate-pair libraries . Additionally the program provides the ability to model both site a…
☆68Sep 10, 2014Updated 11 years ago
Alternatives and similar repositories for SimSeq
Users that are interested in SimSeq are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Experiments for "Scaling read aligners to hundreds of threads on general-purpose processors"☆11Jun 8, 2018Updated 7 years ago
- Reads simulator☆283Sep 3, 2021Updated 4 years ago
- A loose collection of scripts and utilities for processing and analyzing the Goat reference genome assembly☆11Feb 28, 2017Updated 9 years ago
- Specifications for PacBio® native file formats☆31Nov 19, 2024Updated last year
- Preprocessing paired-end reads produced with experiment-specific protocols☆32Jun 28, 2018Updated 7 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Improved Phased Assembler☆28Mar 11, 2022Updated 4 years ago
- ☆12Sep 11, 2025Updated 7 months ago
- Tool for assessing/improving assembly quality in extra-long tandem repeats☆49Feb 23, 2021Updated 5 years ago
- Validate FastQ Files☆36Oct 30, 2018Updated 7 years ago
- Parallel k-mer indexing for biological sequences☆12Dec 14, 2018Updated 7 years ago
- Genome assembly scaffolding using information from paired-end/mate-pair libraries, long reads, and synteny to closely related species.☆24Dec 6, 2018Updated 7 years ago
- Guided synteny alignment between duplicated genomes (within specified quota constraint)☆59Sep 5, 2017Updated 8 years ago
- Read nanopore sequence reads in real-time☆14Feb 9, 2017Updated 9 years ago
- 10x Genomics Linked-Read Alignment, Variant Calling, Phasing, and Structural Variant Calling☆33Jul 31, 2020Updated 5 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- The repository keeps the files for an IPython notebook on about how to make a simple genome assembler using python☆30May 10, 2018Updated 7 years ago
- ☆15Apr 19, 2018Updated 8 years ago
- Tools for improving the sensitivity and specificity of genome alignments☆58Mar 12, 2026Updated last month
- SVsim: a tool that generates synthetic Structural Variant calls as benchmarks to test/evaluate SV calling pipelines.☆18Dec 4, 2017Updated 8 years ago
- StriDe Assembler☆25Nov 23, 2017Updated 8 years ago
- A efficient method to construct BWT index of a given DNA sequence, especially useful for gigantic and high similar genome.☆15May 4, 2016Updated 9 years ago
- GAPPadder is tool for closing gaps on draft genomes with short sequencing data☆28Jun 1, 2017Updated 8 years ago
- Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr…☆297May 9, 2024Updated last year
- DNA copy number detection from off-target sequence data☆34May 17, 2018Updated 7 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- PgRC: Pseudogenome based Read Compressor☆14Nov 20, 2024Updated last year
- Efficient base quality score recalibrator for NGS data☆24Nov 28, 2015Updated 10 years ago
- Chromosome Scale Assembler: A high-throughput chromosome scale genome assembly pipeline for vertebrate genomes☆10Oct 16, 2024Updated last year
- Variant Calling and Postfiltering☆11Jan 9, 2017Updated 9 years ago
- Workflows for correcting and scaffolding long-read (PacBio, nanopore) genome assemblies using optical mapping and/or Dovetail Hi-C data☆20Aug 18, 2020Updated 5 years ago
- RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag☆174May 30, 2021Updated 4 years ago
- add DNA sequence motifs to ggplot☆13Jun 20, 2018Updated 7 years ago
- De novo assembly of nanopore reads using nextflow☆20Aug 5, 2020Updated 5 years ago
- Tools for early stage alignment file processing☆96Mar 12, 2019Updated 7 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Long-read metagenomic analysis☆111Oct 10, 2023Updated 2 years ago
- A pipeline for primary analysis of shotgun metagenomic sequencing data☆11Jun 10, 2019Updated 6 years ago
- Run-length compressed BWT with LZ77 sampled suffix array☆10Apr 25, 2022Updated 4 years ago
- ☆12Updated this week
- A framework to annotate SVs with previous known SVs (vcf file) and or with genomic features (gff and or bed files)☆13Mar 12, 2018Updated 8 years ago
- Long Reads Annotation pipeline☆73Mar 31, 2022Updated 4 years ago
- Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish☆57Jan 26, 2023Updated 3 years ago