Genome Assembly Pipeline: SMARTdenovo

Posted on 2018-04-23 | In genome assembly , TGS pipeline | | Views:

| 3.1k | 0:03

Introduction From its Git Repo: SMARTdenovo is a de novo assembler for PacBio and Oxford Nanopore (ONT) data. It produces an assembly from all-vs-al ...

Identify circRNAs and Fusions from RNA-seq Using STARChip

Posted on 2018-04-23 | In RNA-seq , circRNA | | Views:

| 16k | 0:14

I want to find out some circRNAs from RNA-seq data (total RNA-seq, not poly-A enriched). There are many tools for this mission. Here is a good review ...

How to Install Perl Modules

Posted on 2018-04-13 | In mixture | | Views:

| 8.9k | 0:08

Installing perl modules can be troublesome, especially when you’re not a ROOT user. After a lot of “pain”, I decide to document the two ways to instal ...

Genome Assembly Pipeline: Flye

Posted on 2018-03-30 | In genome assembly , TGS pipeline | | Views:

| 8.9k | 0:08

Intro From its git repo: Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. Th ...

Genome Assembly Pipeline: miniasm & Racon

Posted on 2018-03-30 | In genome assembly , TGS pipeline | | Views:

| 12k | 0:11

miniasm + Racon is a long-read de novo genome assembly pipeline. miniasm + Racon assembly pipeline There are two good examples: Assembly using minia ...

Genome Assembly Pipeline: OPERA-LG

Posted on 2018-03-30 | In genome assembly , TGS pipeline | | Views:

| 6.3k | 0:06

Genome assembly pipeline: OPERA-LG tags: bio-tools, genome assembly pipeline, hybrid genome assembly, scaffloding category: genome assembly, hyrid pi ...

Genome Assembly Pipeline: BESST

Posted on 2018-03-30 | In genome assembly , NGS pipeline | | Views:

| 3.1k | 0:03

Intro From the introduction of BESST git repo: BESST is a package for scaffolding genomic assemblies. It paper Sahlin K, Chikhi R, Arvestad L. Ass ...

Genome Assembly Pipeline: LINKS

Posted on 2018-03-30 | In genome assembly , hybrid pipeline | | Views:

| 11k | 0:10

Intro From its Git Repo LINKS is a scalable genomics application for scaffolding or re-scaffolding genome assembly drafts with long reads, such as t ...

Genome Assembly Pipeline: MEGAHIT & SOAPdenovo-fusion

Posted on 2018-03-29 | In genome assembly , NGS pipeline | | Views:

| 11k | 0:10

MEGAHIT can be used to assemble contigs, and SOAPdenovo-fusion can be used for scaffolding. Since they were developed by the same team, I just put the ...

Upstream Analysis of TCR/BCR Repertoires in RNA-seq Data

Posted on 2018-03-29 | In RNA-seq , immune , TCR/BCR | | Views:

| 11k | 0:10

Bacground: because the transcriptome data I recently worked with is highly related with immune. So I want to dig out something about immune. When I vi ...